From 3b967f722af20e027a57d075c0f027a580733819 Mon Sep 17 00:00:00 2001 From: Macabe Wood Date: Mon, 18 May 2026 16:08:54 -0700 Subject: [PATCH 01/15] refactoring transformers to allow ancmobc2_visualizer to take ancombc results --- q2_composition/_ancombc2.py | 14 +- .../_ancombc2_visualizer/package-lock.json | 139 +++++++++++++++++- .../_ancombc2_visualizer/package.json | 9 +- .../_ancombc2_visualizer/src/App.svelte | 2 - q2_composition/_transformer.py | 108 +++++++++++++- q2_composition/plugin_setup.py | 3 +- 6 files changed, 252 insertions(+), 23 deletions(-) diff --git a/q2_composition/_ancombc2.py b/q2_composition/_ancombc2.py index f4f3fc8..4725509 100644 --- a/q2_composition/_ancombc2.py +++ b/q2_composition/_ancombc2.py @@ -26,8 +26,12 @@ import qiime2 from qiime2.metadata import NumericMetadataColumn, CategoricalMetadataColumn from qiime2.plugin.util import transform +from typing import Union + +from q2_composition._format import ( + ANCOMBC2OutputDirFmt, ANCOMBC2SliceMapping, DataLoafPackageDirFmt +) -from q2_composition._format import ANCOMBC2OutputDirFmt, ANCOMBC2SliceMapping r_base = importr('base') r_stats = importr('stats') @@ -850,10 +854,9 @@ def _rename(column: str) -> str: return structural_zeros_df.rename(lambda c: _rename(c), axis='columns') - def ancombc2_visualizer( output_dir: str, - data: ANCOMBC2OutputDirFmt, + data: Union[ANCOMBC2OutputDirFmt, DataLoafPackageDirFmt], taxonomy: pd.DataFrame = None ): ''' @@ -884,7 +887,10 @@ def ancombc2_visualizer( if taxonomy is not None: # subset taxonomy to only features present in the ancombc2 slices slice_map = transform(data=data, to_type=ANCOMBC2SliceMapping) - slice_feature_ids = slice_map['lfc']['taxon'].unique() + try: + slice_feature_ids = slice_map['lfc']['taxon'].unique() + except KeyError: + slice_feature_ids = slice_map['lfc']['id'].unique() taxonomy = taxonomy[taxonomy.index.isin(slice_feature_ids)] if len(taxonomy) == 0: diff --git a/q2_composition/_ancombc2_visualizer/package-lock.json b/q2_composition/_ancombc2_visualizer/package-lock.json index f2f32dd..e3c5ec0 100644 --- a/q2_composition/_ancombc2_visualizer/package-lock.json +++ b/q2_composition/_ancombc2_visualizer/package-lock.json @@ -8,7 +8,8 @@ "name": "diverging-barplot", "version": "0.0.0", "dependencies": { - "d3": "^7.9.0" + "d3": "^7.9.0", + "ts-node": "^10.9.2" }, "devDependencies": { "@sveltejs/vite-plugin-svelte": "^5.0.3", @@ -24,6 +25,26 @@ "vitest": "^2.1.8" } }, + "node_modules/@cspotcode/source-map-support": { + "version": "0.8.1", + "resolved": "https://registry.npmjs.org/@cspotcode/source-map-support/-/source-map-support-0.8.1.tgz", + "integrity": "sha512-IchNf6dN4tHoMFIn/7OE8LWZ19Y6q/67Bmf6vnGREv8RSbBVb9LPJxEcnwrcwX6ixSvaiGoomAUvu4YSxXrVgw==", + "dependencies": { + "@jridgewell/trace-mapping": "0.3.9" + }, + "engines": { + "node": ">=12" + } + }, + "node_modules/@cspotcode/source-map-support/node_modules/@jridgewell/trace-mapping": { + "version": "0.3.9", + "resolved": "https://registry.npmjs.org/@jridgewell/trace-mapping/-/trace-mapping-0.3.9.tgz", + "integrity": "sha512-3Belt6tdc8bPgAtbcmdtNJlirVoTmEb5e2gC94PnkwEW9jI6CAHUeoG85tjWP5WquqfavoMtMwiG4P926ZKKuQ==", + "dependencies": { + "@jridgewell/resolve-uri": "^3.0.3", + "@jridgewell/sourcemap-codec": "^1.4.10" + } + }, "node_modules/@esbuild/aix-ppc64": { "version": "0.25.9", "resolved": "https://registry.npmjs.org/@esbuild/aix-ppc64/-/aix-ppc64-0.25.9.tgz", @@ -492,7 +513,6 @@ "version": "3.1.2", "resolved": "https://registry.npmjs.org/@jridgewell/resolve-uri/-/resolve-uri-3.1.2.tgz", "integrity": "sha512-bRISgCIjP20/tbWSPWMEi54QVPRZExkuD9lJL+UIxUKtwVJA8wW1Trb1jMs1RFXo1CBTNZ/5hpC9QvmKWdopKw==", - "dev": true, "license": "MIT", "engines": { "node": ">=6.0.0" @@ -502,7 +522,6 @@ "version": "1.5.0", "resolved": "https://registry.npmjs.org/@jridgewell/sourcemap-codec/-/sourcemap-codec-1.5.0.tgz", "integrity": "sha512-gv3ZRaISU3fjPAgNsriBRqGWQL6quFx04YMPW/zD8XMLsU32mhCCbfbO6KZFLjvYpCZ8zyDEgqsgf+PwPaM7GQ==", - "dev": true, "license": "MIT" }, "node_modules/@jridgewell/trace-mapping": { @@ -1174,6 +1193,26 @@ "vite": "^5.2.0 || ^6" } }, + "node_modules/@tsconfig/node10": { + "version": "1.0.12", + "resolved": "https://registry.npmjs.org/@tsconfig/node10/-/node10-1.0.12.tgz", + "integrity": "sha512-UCYBaeFvM11aU2y3YPZ//O5Rhj+xKyzy7mvcIoAjASbigy8mHMryP5cK7dgjlz2hWxh1g5pLw084E0a/wlUSFQ==" + }, + "node_modules/@tsconfig/node12": { + "version": "1.0.11", + "resolved": "https://registry.npmjs.org/@tsconfig/node12/-/node12-1.0.11.tgz", + "integrity": "sha512-cqefuRsh12pWyGsIoBKJA9luFu3mRxCA+ORZvA4ktLSzIuCUtWVxGIuXigEwO5/ywWFMZ2QEGKWvkZG1zDMTag==" + }, + "node_modules/@tsconfig/node14": { + "version": "1.0.3", + "resolved": "https://registry.npmjs.org/@tsconfig/node14/-/node14-1.0.3.tgz", + "integrity": "sha512-ysT8mhdixWK6Hw3i1V2AeRqZ5WfXg1G43mqoYlM2nc6388Fq5jcXyr5mRsqViLx/GJYdoL0bfXD8nmF+Zn/Iow==" + }, + "node_modules/@tsconfig/node16": { + "version": "1.0.4", + "resolved": "https://registry.npmjs.org/@tsconfig/node16/-/node16-1.0.4.tgz", + "integrity": "sha512-vxhUy4J8lyeyinH7Azl1pdd43GJhZH/tP2weN8TntQblOY+A0XbT8DJk1/oCPuOOyg/Ja757rG0CgHcWC8OfMA==" + }, "node_modules/@tsconfig/svelte": { "version": "5.0.4", "resolved": "https://registry.npmjs.org/@tsconfig/svelte/-/svelte-5.0.4.tgz", @@ -1483,7 +1522,6 @@ "version": "22.12.0", "resolved": "https://registry.npmjs.org/@types/node/-/node-22.12.0.tgz", "integrity": "sha512-Fll2FZ1riMjNmlmJOdAyY5pUbkftXslB5DgEzlIuNaiWhXd00FhWxVC/r4yV/4wBb9JfImTu+jiSvXTkJ7F/gA==", - "dev": true, "license": "MIT", "dependencies": { "undici-types": "~6.20.0" @@ -1586,7 +1624,6 @@ "version": "8.16.0", "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.16.0.tgz", "integrity": "sha512-UVJyE9MttOsBQIDKw1skb9nAwQuR5wuGD3+82K6JgJlm/Y+KI92oNsMNGZCYdDsVtRHSak0pcV5Dno5+4jh9sw==", - "dev": true, "license": "MIT", "bin": { "acorn": "bin/acorn" @@ -1595,6 +1632,22 @@ "node": ">=0.4.0" } }, + "node_modules/acorn-walk": { + "version": "8.3.5", + "resolved": "https://registry.npmjs.org/acorn-walk/-/acorn-walk-8.3.5.tgz", + "integrity": "sha512-HEHNfbars9v4pgpW6SO1KSPkfoS0xVOM/9UzkJltjlsHZmJasxg8aXkuZa7SMf8vKGIBhpUsPluQSqhJFCqebw==", + "dependencies": { + "acorn": "^8.11.0" + }, + "engines": { + "node": ">=0.4.0" + } + }, + "node_modules/arg": { + "version": "4.1.3", + "resolved": "https://registry.npmjs.org/arg/-/arg-4.1.3.tgz", + "integrity": "sha512-58S9QDqG0Xx27YwPSt9fJxivjYl432YCwfDMfZ+71RAqUrZef7LrKQZ3LHLOwCS4FLNBplP533Zx895SeOCHvA==" + }, "node_modules/aria-query": { "version": "5.3.2", "resolved": "https://registry.npmjs.org/aria-query/-/aria-query-5.3.2.tgz", @@ -1697,6 +1750,11 @@ "node": ">= 10" } }, + "node_modules/create-require": { + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/create-require/-/create-require-1.1.1.tgz", + "integrity": "sha512-dcKFX3jn0MpIaXjisoRvexIJVEKzaq7z2rZKxf+MSr9TkdmHmsU4m2lcLojrj/FHl8mk5VxMmYA+ftRkP/3oKQ==" + }, "node_modules/d3": { "version": "7.9.0", "resolved": "https://registry.npmjs.org/d3/-/d3-7.9.0.tgz", @@ -2161,6 +2219,14 @@ "dev": true, "license": "MIT" }, + "node_modules/diff": { + "version": "4.0.4", + "resolved": "https://registry.npmjs.org/diff/-/diff-4.0.4.tgz", + "integrity": "sha512-X07nttJQkwkfKfvTPG/KSnE2OMdcUCao6+eXF3wmnIQRn2aPAHH3VxDbDOdegkd6JbPsXqShpvEOHfAT+nCNwQ==", + "engines": { + "node": ">=0.3.1" + } + }, "node_modules/enhanced-resolve": { "version": "5.18.1", "resolved": "https://registry.npmjs.org/enhanced-resolve/-/enhanced-resolve-5.18.1.tgz", @@ -2601,6 +2667,11 @@ "@jridgewell/sourcemap-codec": "^1.5.0" } }, + "node_modules/make-error": { + "version": "1.3.6", + "resolved": "https://registry.npmjs.org/make-error/-/make-error-1.3.6.tgz", + "integrity": "sha512-s8UhlNe7vPKomQhC1qFelMokr/Sc3AgNbso3n74mVPA5LTZwkB9NlXf4XPamLxJE8h0gh73rM94xvwRT2CVInw==" + }, "node_modules/mri": { "version": "1.2.0", "resolved": "https://registry.npmjs.org/mri/-/mri-1.2.0.tgz", @@ -2948,12 +3019,52 @@ "node": ">=14.0.0" } }, + "node_modules/ts-node": { + "version": "10.9.2", + "resolved": "https://registry.npmjs.org/ts-node/-/ts-node-10.9.2.tgz", + "integrity": "sha512-f0FFpIdcHgn8zcPSbf1dRevwt047YMnaiJM3u2w2RewrB+fob/zePZcrOyQoLMMO7aBIddLcQIEK5dYjkLnGrQ==", + "dependencies": { + "@cspotcode/source-map-support": "^0.8.0", + "@tsconfig/node10": "^1.0.7", + "@tsconfig/node12": "^1.0.7", + "@tsconfig/node14": "^1.0.0", + "@tsconfig/node16": "^1.0.2", + "acorn": "^8.4.1", + "acorn-walk": "^8.1.1", + "arg": "^4.1.0", + "create-require": "^1.1.0", + "diff": "^4.0.1", + "make-error": "^1.1.1", + "v8-compile-cache-lib": "^3.0.1", + "yn": "3.1.1" + }, + "bin": { + "ts-node": "dist/bin.js", + "ts-node-cwd": "dist/bin-cwd.js", + "ts-node-esm": "dist/bin-esm.js", + "ts-node-script": "dist/bin-script.js", + "ts-node-transpile-only": "dist/bin-transpile.js", + "ts-script": "dist/bin-script-deprecated.js" + }, + "peerDependencies": { + "@swc/core": ">=1.2.50", + "@swc/wasm": ">=1.2.50", + "@types/node": "*", + "typescript": ">=2.7" + }, + "peerDependenciesMeta": { + "@swc/core": { + "optional": true + }, + "@swc/wasm": { + "optional": true + } + } + }, "node_modules/typescript": { "version": "5.6.3", "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.6.3.tgz", "integrity": "sha512-hjcS1mhfuyi4WW8IWtjP7brDrG2cuDZukyrYrSauoXGNgx0S7zceP07adYkJycEr56BOUTNPzbInooiN3fn1qw==", - "dev": true, - "license": "Apache-2.0", "bin": { "tsc": "bin/tsc", "tsserver": "bin/tsserver" @@ -2966,9 +3077,13 @@ "version": "6.20.0", "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-6.20.0.tgz", "integrity": "sha512-Ny6QZ2Nju20vw1SRHe3d9jVu6gJ+4e3+MMpqu7pqE5HT6WsTSlce++GQmK5UXS8mzV8DSYHrQH+Xrf2jVcuKNg==", - "dev": true, "license": "MIT" }, + "node_modules/v8-compile-cache-lib": { + "version": "3.0.1", + "resolved": "https://registry.npmjs.org/v8-compile-cache-lib/-/v8-compile-cache-lib-3.0.1.tgz", + "integrity": "sha512-wa7YjyUGfNZngI/vtK0UHAN+lgDCxBPCylVXGp0zu59Fz5aiGtNXaq3DhIov063MorB+VfufLh3JlF2KdTK3xg==" + }, "node_modules/vite": { "version": "6.4.1", "resolved": "https://registry.npmjs.org/vite/-/vite-6.4.1.tgz", @@ -4176,6 +4291,14 @@ "node": ">=8" } }, + "node_modules/yn": { + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", + "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", + "engines": { + "node": ">=6" + } + }, "node_modules/zimmerframe": { "version": "1.1.2", "resolved": "https://registry.npmjs.org/zimmerframe/-/zimmerframe-1.1.2.tgz", diff --git a/q2_composition/_ancombc2_visualizer/package.json b/q2_composition/_ancombc2_visualizer/package.json index 1d3103d..fdc86d0 100644 --- a/q2_composition/_ancombc2_visualizer/package.json +++ b/q2_composition/_ancombc2_visualizer/package.json @@ -12,18 +12,19 @@ }, "devDependencies": { "@sveltejs/vite-plugin-svelte": "^5.0.3", + "@tailwindcss/vite": "^4.1.4", "@tsconfig/svelte": "^5.0.4", "@types/d3": "^7.4.3", "@types/node": "^22.10.5", "svelte": "^5.53.0", "svelte-check": "^4.1.1", + "tailwindcss": "^4.1.4", "typescript": "~5.6.2", "vite": "^6.4.1", - "vitest": "^2.1.8", - "@tailwindcss/vite": "^4.1.4", - "tailwindcss": "^4.1.4" + "vitest": "^2.1.8" }, "dependencies": { - "d3": "^7.9.0" + "d3": "^7.9.0", + "ts-node": "^10.9.2" } } diff --git a/q2_composition/_ancombc2_visualizer/src/App.svelte b/q2_composition/_ancombc2_visualizer/src/App.svelte index d14cd27..8099442 100644 --- a/q2_composition/_ancombc2_visualizer/src/App.svelte +++ b/q2_composition/_ancombc2_visualizer/src/App.svelte @@ -12,9 +12,7 @@ const fetchPromise = fetch(taxonomyPath); const taxonomyPromise = fetchPromise.then((response) => { - console.log("response", response); if (response.ok) { - console.log("parsing taxonomy"); return parseTaxonomy(taxonomyPath); } else { return Promise.resolve(null); diff --git a/q2_composition/_transformer.py b/q2_composition/_transformer.py index 70cb2ac..9c1b796 100644 --- a/q2_composition/_transformer.py +++ b/q2_composition/_transformer.py @@ -7,6 +7,7 @@ # ---------------------------------------------------------------------------- import json +import os import pandas as pd @@ -41,9 +42,17 @@ def _12(format: DataLoafPackageDirFmt) -> ANCOMBC2SliceMapping: slices = ANCOMBC2SliceMapping() slices.intercepts = intercepts - + + name_map = { + 'lfc': 'lfc', + 'se': 'se', + 'p_val': 'p', + 'q_val': 'q', + 'w': 'W', + } for (slice_path, slice_df) in format.data_slices.iter_views(pd.DataFrame): - slice_name = slice_path.name.split('_slice')[0] + slice_name = name_map[slice_path.name.split('_slice')[0]] + slice_df = slice_df.rename(columns={'id': 'taxon'}) slices[slice_name] = slice_df return slices @@ -59,8 +68,34 @@ def _2(slices: ANCOMBC2SliceMapping) -> ANCOMBC2OutputDirFmt: for slice_name, slice_df in slices.items(): format_slice = format.__getattribute__(slice_name) format_slice.write_data(slice_df, pd.DataFrame) - - return format + + extra_files = ['diff', 'passed_ss'] + if not any(file in slices.keys() for file in extra_files): + header = { + "doctype": { + "name": "table.jsonl", + "format": "application/x-json-lines", + "version": "1.0" + }, + "direction": "row", + "style": "key:value", + "fields": [ + {"name": "taxon", "type": "string", "missing": False}, + {"name": "(Intercept)", "type": "number", "missing": False} + ], + "index": [], + "title": "", + "description": "", + "extra": {} + } + + for file in extra_files: + output_path = os.path.join(format.path, file + '.jsonl') + with open(output_path, 'w') as f: + f.write(json.dumps(header, separators=(',', ':')) + "\n") + + + return format @plugin.register_transformer @@ -94,3 +129,68 @@ def _3(format: ANCOMBC2OutputDirFmt) -> ANCOMBC2SliceMapping: slices.intercepts = list(intercepts) return slices + +@plugin.register_transformer +def _5(format:DataLoafPackageDirFmt) -> ANCOMBC2OutputDirFmt: + slice_format = _12(format) + ancombc2_format = _2(slice_format) + return ancombc2_format + + +# @plugin.register_transformer +# def _4(format: DataLoafPackageDirFmt) -> ANCOMBC2OutputDirFmt: +# ANCOMBC2_output = ANCOMBC2OutputDirFmt() + +# header = { +# "doctype": { +# "name": "table.jsonl", +# "format": "application/x-json-lines", +# "version": "1.0" +# }, +# "direction": "row", +# "style": "key:value", +# "fields": [ +# {"name": "taxon", "type": "string", "missing": False}, +# {"name": "(Intercept)", "type": "number", "missing": False} +# ], +# "index": [], +# "title": "", +# "description": "", +# "extra": {} +# } + +# for file in os.listdir(format.path): +# if not file.endswith('.csv'): +# continue + +# input_path = os.path.join(format.path, file) +# file_name = str(file).replace('_slice.csv', '') +# file_name = file_name.replace('_val', '') +# if file_name == 'w': +# file_name = file_name.upper() +# file_name = file_name + '.jsonl' +# output_path = os.path.join(ANCOMBC2_output.path, file_name) + +# df = pd.read_csv(input_path) +# json_file = df.to_json(output_path) + +# json_file = json.load(open(output_path)) +# n = len(json_file["id"]) + +# with open(output_path, "w") as f: +# f.write(json.dumps(header, separators=(',', ':')) + "\n") + +# for i in range(n): +# row = { +# "taxon": json_file["id"][str(i)], +# "(Intercept)": json_file["(Intercept)"][str(i)] +# } +# f.write(json.dumps(row) + "\n") + +# extra_files = ['diff.jsonl', 'passed_ss.jsonl'] +# for file in extra_files: +# output_path = os.path.join(ANCOMBC2_output.path, file) +# with open(output_path, 'w') as f: +# f.write(json.dumps(header, separators=(',', ':')) + "\n") + +# return ANCOMBC2_output diff --git a/q2_composition/plugin_setup.py b/q2_composition/plugin_setup.py index 538d4fc..86111e9 100644 --- a/q2_composition/plugin_setup.py +++ b/q2_composition/plugin_setup.py @@ -6,6 +6,7 @@ # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- +import qiime2 import importlib import numpy as np @@ -293,7 +294,7 @@ plugin.visualizers.register_function( function=q2_composition.ancombc2_visualizer, inputs={ - 'data': FeatureData[ANCOMBC2Output], + 'data': FeatureData[DifferentialAbundance | ANCOMBC2Output], 'taxonomy': FeatureData[Taxonomy], }, parameters={}, From 5eed7deb093e2513a78dfd65283874c3752457c6 Mon Sep 17 00:00:00 2001 From: Macabe Wood Date: Mon, 18 May 2026 16:14:23 -0700 Subject: [PATCH 02/15] lint --- q2_composition/_ancombc2.py | 1 + q2_composition/_transformer.py | 73 ++++------------------------------ q2_composition/plugin_setup.py | 1 - 3 files changed, 8 insertions(+), 67 deletions(-) diff --git a/q2_composition/_ancombc2.py b/q2_composition/_ancombc2.py index 4725509..8a34ab6 100644 --- a/q2_composition/_ancombc2.py +++ b/q2_composition/_ancombc2.py @@ -854,6 +854,7 @@ def _rename(column: str) -> str: return structural_zeros_df.rename(lambda c: _rename(c), axis='columns') + def ancombc2_visualizer( output_dir: str, data: Union[ANCOMBC2OutputDirFmt, DataLoafPackageDirFmt], diff --git a/q2_composition/_transformer.py b/q2_composition/_transformer.py index 9c1b796..c60c3f7 100644 --- a/q2_composition/_transformer.py +++ b/q2_composition/_transformer.py @@ -42,7 +42,7 @@ def _12(format: DataLoafPackageDirFmt) -> ANCOMBC2SliceMapping: slices = ANCOMBC2SliceMapping() slices.intercepts = intercepts - + name_map = { 'lfc': 'lfc', 'se': 'se', @@ -68,7 +68,7 @@ def _2(slices: ANCOMBC2SliceMapping) -> ANCOMBC2OutputDirFmt: for slice_name, slice_df in slices.items(): format_slice = format.__getattribute__(slice_name) format_slice.write_data(slice_df, pd.DataFrame) - + extra_files = ['diff', 'passed_ss'] if not any(file in slices.keys() for file in extra_files): header = { @@ -88,13 +88,12 @@ def _2(slices: ANCOMBC2SliceMapping) -> ANCOMBC2OutputDirFmt: "description": "", "extra": {} } - + for file in extra_files: output_path = os.path.join(format.path, file + '.jsonl') with open(output_path, 'w') as f: - f.write(json.dumps(header, separators=(',', ':')) + "\n") - - + f.write(json.dumps(header, separators=(',', ':')) + "\n") + return format @@ -130,67 +129,9 @@ def _3(format: ANCOMBC2OutputDirFmt) -> ANCOMBC2SliceMapping: return slices + @plugin.register_transformer -def _5(format:DataLoafPackageDirFmt) -> ANCOMBC2OutputDirFmt: +def _5(format: DataLoafPackageDirFmt) -> ANCOMBC2OutputDirFmt: slice_format = _12(format) ancombc2_format = _2(slice_format) return ancombc2_format - - -# @plugin.register_transformer -# def _4(format: DataLoafPackageDirFmt) -> ANCOMBC2OutputDirFmt: -# ANCOMBC2_output = ANCOMBC2OutputDirFmt() - -# header = { -# "doctype": { -# "name": "table.jsonl", -# "format": "application/x-json-lines", -# "version": "1.0" -# }, -# "direction": "row", -# "style": "key:value", -# "fields": [ -# {"name": "taxon", "type": "string", "missing": False}, -# {"name": "(Intercept)", "type": "number", "missing": False} -# ], -# "index": [], -# "title": "", -# "description": "", -# "extra": {} -# } - -# for file in os.listdir(format.path): -# if not file.endswith('.csv'): -# continue - -# input_path = os.path.join(format.path, file) -# file_name = str(file).replace('_slice.csv', '') -# file_name = file_name.replace('_val', '') -# if file_name == 'w': -# file_name = file_name.upper() -# file_name = file_name + '.jsonl' -# output_path = os.path.join(ANCOMBC2_output.path, file_name) - -# df = pd.read_csv(input_path) -# json_file = df.to_json(output_path) - -# json_file = json.load(open(output_path)) -# n = len(json_file["id"]) - -# with open(output_path, "w") as f: -# f.write(json.dumps(header, separators=(',', ':')) + "\n") - -# for i in range(n): -# row = { -# "taxon": json_file["id"][str(i)], -# "(Intercept)": json_file["(Intercept)"][str(i)] -# } -# f.write(json.dumps(row) + "\n") - -# extra_files = ['diff.jsonl', 'passed_ss.jsonl'] -# for file in extra_files: -# output_path = os.path.join(ANCOMBC2_output.path, file) -# with open(output_path, 'w') as f: -# f.write(json.dumps(header, separators=(',', ':')) + "\n") - -# return ANCOMBC2_output diff --git a/q2_composition/plugin_setup.py b/q2_composition/plugin_setup.py index 86111e9..e374399 100644 --- a/q2_composition/plugin_setup.py +++ b/q2_composition/plugin_setup.py @@ -6,7 +6,6 @@ # The full license is in the file LICENSE, distributed with this software. # ---------------------------------------------------------------------------- -import qiime2 import importlib import numpy as np From a295c33a7c3579782a13ab6153270a6d5ea134b8 Mon Sep 17 00:00:00 2001 From: Macabe Wood Date: Tue, 19 May 2026 10:45:56 -0700 Subject: [PATCH 03/15] Small fix --- q2_composition/_transformer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/q2_composition/_transformer.py b/q2_composition/_transformer.py index c60c3f7..2aae9f8 100644 --- a/q2_composition/_transformer.py +++ b/q2_composition/_transformer.py @@ -94,7 +94,7 @@ def _2(slices: ANCOMBC2SliceMapping) -> ANCOMBC2OutputDirFmt: with open(output_path, 'w') as f: f.write(json.dumps(header, separators=(',', ':')) + "\n") - return format + return format @plugin.register_transformer From f56c159b7bfcaabfe1170e8c4d64b58b1a3a19eb Mon Sep 17 00:00:00 2001 From: Macabe Wood Date: Tue, 19 May 2026 14:16:24 -0700 Subject: [PATCH 04/15] Delating original da-barplot renaming amcombc-viz to da-barplot --- Makefile | 10 +- q2_composition/__init__.py | 6 +- q2_composition/_ancombc2.py | 5 +- q2_composition/_da_barplot/.gitignore | 26 + .../_da_barplot/.vscode/extensions.json | 3 + q2_composition/_da_barplot/index.html | 14 + q2_composition/_da_barplot/package-lock.json | 4187 +++++++++++++++++ q2_composition/_da_barplot/package.json | 29 + q2_composition/_da_barplot/src/App.svelte | 63 + q2_composition/_da_barplot/src/app.css | 12 + .../_da_barplot/src/lib/Barplot.svelte | 47 + .../src/lib/BarplotControls.svelte | 82 + .../_da_barplot/src/lib/BarplotFilters.svelte | 157 + .../src/lib/ControlContainer.svelte | 8 + .../_da_barplot/src/lib/SelectedTaxon.svelte | 147 + .../_da_barplot/src/lib/Taxonomy.svelte | 37 + .../_da_barplot/src/lib/TaxonomyFilter.svelte | 99 + .../src/lib/TaxonomyFilterList.svelte | 137 + q2_composition/_da_barplot/src/main.ts | 9 + .../_da_barplot/src/util/features.svelte.ts | 309 ++ q2_composition/_da_barplot/src/util/parse.ts | 148 + q2_composition/_da_barplot/src/util/plot.ts | 526 +++ .../_da_barplot/src/util/taxonomy.svelte.ts | 729 +++ q2_composition/_da_barplot/src/vite-env.d.ts | 2 + q2_composition/_da_barplot/svelte.config.js | 7 + .../tests/data/output-format/W.jsonl | 9 + .../tests/data/output-format/diff.jsonl | 9 + .../tests/data/output-format/lfc.jsonl | 9 + .../tests/data/output-format/p.jsonl | 9 + .../tests/data/output-format/passed_ss.jsonl | 9 + .../tests/data/output-format/q.jsonl | 9 + .../tests/data/output-format/se.jsonl | 9 + .../data/output-format/structural-zeros.jsonl | 771 +++ .../_da_barplot/tests/data/taxonomy-fake.tsv | 8 + .../_da_barplot/tests/data/taxonomy.tsv | 771 +++ .../_da_barplot/tests/featureRecord.test.ts | 93 + .../_da_barplot/tests/parse.test.ts | 168 + .../_da_barplot/tests/taxonomy.test.ts | 52 + q2_composition/_da_barplot/tsconfig.app.json | 20 + q2_composition/_da_barplot/tsconfig.json | 7 + q2_composition/_da_barplot/tsconfig.node.json | 24 + q2_composition/_da_barplot/vite.config.ts | 9 + q2_composition/_diff_abundance_plots.py | 242 - q2_composition/plugin_setup.py | 61 +- q2_composition/tests/test_ancombc2.py | 12 +- .../tests/test_diff_abundance_plot.py | 564 --- 46 files changed, 8787 insertions(+), 877 deletions(-) create mode 100644 q2_composition/_da_barplot/.gitignore create mode 100644 q2_composition/_da_barplot/.vscode/extensions.json create mode 100644 q2_composition/_da_barplot/index.html create mode 100644 q2_composition/_da_barplot/package-lock.json create mode 100644 q2_composition/_da_barplot/package.json create mode 100644 q2_composition/_da_barplot/src/App.svelte create mode 100644 q2_composition/_da_barplot/src/app.css create mode 100644 q2_composition/_da_barplot/src/lib/Barplot.svelte create mode 100644 q2_composition/_da_barplot/src/lib/BarplotControls.svelte create mode 100644 q2_composition/_da_barplot/src/lib/BarplotFilters.svelte create mode 100644 q2_composition/_da_barplot/src/lib/ControlContainer.svelte create mode 100644 q2_composition/_da_barplot/src/lib/SelectedTaxon.svelte create mode 100644 q2_composition/_da_barplot/src/lib/Taxonomy.svelte create mode 100644 q2_composition/_da_barplot/src/lib/TaxonomyFilter.svelte create mode 100644 q2_composition/_da_barplot/src/lib/TaxonomyFilterList.svelte create mode 100644 q2_composition/_da_barplot/src/main.ts create mode 100644 q2_composition/_da_barplot/src/util/features.svelte.ts create mode 100644 q2_composition/_da_barplot/src/util/parse.ts create mode 100644 q2_composition/_da_barplot/src/util/plot.ts create mode 100644 q2_composition/_da_barplot/src/util/taxonomy.svelte.ts create mode 100644 q2_composition/_da_barplot/src/vite-env.d.ts create mode 100644 q2_composition/_da_barplot/svelte.config.js create mode 100644 q2_composition/_da_barplot/tests/data/output-format/W.jsonl create mode 100644 q2_composition/_da_barplot/tests/data/output-format/diff.jsonl create mode 100644 q2_composition/_da_barplot/tests/data/output-format/lfc.jsonl create mode 100644 q2_composition/_da_barplot/tests/data/output-format/p.jsonl create mode 100644 q2_composition/_da_barplot/tests/data/output-format/passed_ss.jsonl create mode 100644 q2_composition/_da_barplot/tests/data/output-format/q.jsonl create mode 100644 q2_composition/_da_barplot/tests/data/output-format/se.jsonl create mode 100644 q2_composition/_da_barplot/tests/data/output-format/structural-zeros.jsonl create mode 100644 q2_composition/_da_barplot/tests/data/taxonomy-fake.tsv create mode 100644 q2_composition/_da_barplot/tests/data/taxonomy.tsv create mode 100644 q2_composition/_da_barplot/tests/featureRecord.test.ts create mode 100644 q2_composition/_da_barplot/tests/parse.test.ts create mode 100644 q2_composition/_da_barplot/tests/taxonomy.test.ts create mode 100644 q2_composition/_da_barplot/tsconfig.app.json create mode 100644 q2_composition/_da_barplot/tsconfig.json create mode 100644 q2_composition/_da_barplot/tsconfig.node.json create mode 100644 q2_composition/_da_barplot/vite.config.ts delete mode 100644 q2_composition/_diff_abundance_plots.py delete mode 100644 q2_composition/tests/test_diff_abundance_plot.py diff --git a/Makefile b/Makefile index 3b72a15..961755c 100644 --- a/Makefile +++ b/Makefile @@ -21,14 +21,14 @@ dev: all pip install -e . clean: distclean - rm -rf q2_composition/_ancombc2_visualizer/node_modules + rm -rf q2_composition/_da_barplot/node_modules distclean: - rm -rf q2_composition/_ancombc2_visualizer/dist/ + rm -rf q2_composition/_da_barplot/dist/ -q2_composition/_ancombc2_visualizer/dist: - cd q2_composition/_ancombc2_visualizer/ && \ +q2_composition/_da_barplot/dist: + cd q2_composition/_da_barplot/ && \ npm install && \ npm run build -ancombc2-visualizer: q2_composition/_ancombc2_visualizer/dist +ancombc2-visualizer: q2_composition/_da_barplot/dist diff --git a/q2_composition/__init__.py b/q2_composition/__init__.py index d7653aa..c22a93a 100644 --- a/q2_composition/__init__.py +++ b/q2_composition/__init__.py @@ -15,9 +15,8 @@ from ._impute import add_pseudocount from ._ancom import ancom from ._ancombc import ancombc -from ._ancombc2 import ancombc2, ancombc2_visualizer +from ._ancombc2 import ancombc2, da_barplot from ._dataloaf_tabulate import tabulate -from ._diff_abundance_plots import da_barplot try: from ._version import __version__ @@ -27,6 +26,5 @@ __all__ = [ 'FrictionlessCSVFileFormat', 'DataPackageSchemaFileFormat', 'DataLoafPackageDirFmt', 'DifferentialAbundance', 'add_pseudocount', - 'ancom', 'ancombc', 'ancombc2', 'ancombc2_visualizer', 'tabulate', - 'da_barplot' + 'ancom', 'ancombc', 'ancombc2', 'tabulate', 'da_barplot' ] diff --git a/q2_composition/_ancombc2.py b/q2_composition/_ancombc2.py index 8a34ab6..5e2978d 100644 --- a/q2_composition/_ancombc2.py +++ b/q2_composition/_ancombc2.py @@ -32,7 +32,6 @@ ANCOMBC2OutputDirFmt, ANCOMBC2SliceMapping, DataLoafPackageDirFmt ) - r_base = importr('base') r_stats = importr('stats') r_phyloseq = importr('phyloseq') @@ -855,7 +854,7 @@ def _rename(column: str) -> str: return structural_zeros_df.rename(lambda c: _rename(c), axis='columns') -def ancombc2_visualizer( +def da_barplot( output_dir: str, data: Union[ANCOMBC2OutputDirFmt, DataLoafPackageDirFmt], taxonomy: pd.DataFrame = None @@ -881,7 +880,7 @@ def ancombc2_visualizer( dist_dir = ( importlib.resources.files('q2_composition') / - '_ancombc2_visualizer' / 'dist' + '_da_barplot' / 'dist' ) shutil.copytree(Path(str(dist_dir)), output_dir, dirs_exist_ok=True) diff --git a/q2_composition/_da_barplot/.gitignore b/q2_composition/_da_barplot/.gitignore new file mode 100644 index 0000000..775bbdd --- /dev/null +++ b/q2_composition/_da_barplot/.gitignore @@ -0,0 +1,26 @@ +# Logs +logs +*.log +npm-debug.log* +yarn-debug.log* +yarn-error.log* +pnpm-debug.log* +lerna-debug.log* + +node_modules +dist +dist-ssr +*.local + +# Editor directories and files +.vscode/* +!.vscode/extensions.json +.idea +.DS_Store +*.suo +*.ntvs* +*.njsproj +*.sln +*.sw? + +!lib/ diff --git a/q2_composition/_da_barplot/.vscode/extensions.json b/q2_composition/_da_barplot/.vscode/extensions.json new file mode 100644 index 0000000..bdef820 --- /dev/null +++ b/q2_composition/_da_barplot/.vscode/extensions.json @@ -0,0 +1,3 @@ +{ + "recommendations": ["svelte.svelte-vscode"] +} diff --git a/q2_composition/_da_barplot/index.html b/q2_composition/_da_barplot/index.html new file mode 100644 index 0000000..f9207c1 --- /dev/null +++ b/q2_composition/_da_barplot/index.html @@ -0,0 +1,14 @@ + + + + + + + ANCOMBC2 Visualizer + + + +
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"^4.1.1", + "typescript": "~5.6.2", + "vite": "^6.4.1", + "vitest": "^2.1.8", + "@tailwindcss/vite": "^4.1.4", + "tailwindcss": "^4.1.4" + }, + "dependencies": { + "d3": "^7.9.0" + } +} diff --git a/q2_composition/_da_barplot/src/App.svelte b/q2_composition/_da_barplot/src/App.svelte new file mode 100644 index 0000000..d14cd27 --- /dev/null +++ b/q2_composition/_da_barplot/src/App.svelte @@ -0,0 +1,63 @@ + + +
+ {#await featuresPromise} +

Parsing slices...

+ {:then features} + + {:catch error} +

An error occurred: {error.message}

+ {/await} + + {#await taxonomyPromise} +

Parsing taxonomy...

+ {:then rootTaxon} + {#if rootTaxon} + + {/if} + {:catch error} +

An error occurred: {error.message}

+ {/await} +
diff --git a/q2_composition/_da_barplot/src/app.css b/q2_composition/_da_barplot/src/app.css new file mode 100644 index 0000000..592a0a2 --- /dev/null +++ b/q2_composition/_da_barplot/src/app.css @@ -0,0 +1,12 @@ +@import "tailwindcss"; + +button { + @apply px-4 py-1 bg-purple-500 text-white rounded cursor-pointer; +} +button:hover { + @apply bg-purple-600; +} + +button:active { + @apply bg-purple-700; +} \ No newline at end of file diff --git a/q2_composition/_da_barplot/src/lib/Barplot.svelte b/q2_composition/_da_barplot/src/lib/Barplot.svelte new file mode 100644 index 0000000..57ca1d6 --- /dev/null +++ b/q2_composition/_da_barplot/src/lib/Barplot.svelte @@ -0,0 +1,47 @@ + + +
+
+ {#if features.viewVariableLevel != ""} +

+ Reference Level: {referenceLevel} +

+ {/if} + +
+ +
+ + diff --git a/q2_composition/_da_barplot/src/lib/BarplotControls.svelte b/q2_composition/_da_barplot/src/lib/BarplotControls.svelte new file mode 100644 index 0000000..7bcdbf1 --- /dev/null +++ b/q2_composition/_da_barplot/src/lib/BarplotControls.svelte @@ -0,0 +1,82 @@ + + + +
+
+ + +
+
+ + +
+
+

Bar Thickness:

+ + +
+
+ diff --git a/q2_composition/_da_barplot/src/lib/BarplotFilters.svelte b/q2_composition/_da_barplot/src/lib/BarplotFilters.svelte new file mode 100644 index 0000000..755f026 --- /dev/null +++ b/q2_composition/_da_barplot/src/lib/BarplotFilters.svelte @@ -0,0 +1,157 @@ + + + +
+
+ + +
+
+ + +
+
+ + +
+ + + + {#if errorMessage} +

{errorMessage}

+ {/if} +
+ + +{#if filters.length} +
+ {#each filters as filter} +
+

+ {filter.slice} + {getSymbol(filter.relationship)} + {filter.value} +

+ + +
+ {/each} +
+{/if} + + diff --git a/q2_composition/_da_barplot/src/lib/ControlContainer.svelte b/q2_composition/_da_barplot/src/lib/ControlContainer.svelte new file mode 100644 index 0000000..e50f5cf --- /dev/null +++ b/q2_composition/_da_barplot/src/lib/ControlContainer.svelte @@ -0,0 +1,8 @@ + + +
+

{title}

+
{@render children()}
+
diff --git a/q2_composition/_da_barplot/src/lib/SelectedTaxon.svelte b/q2_composition/_da_barplot/src/lib/SelectedTaxon.svelte new file mode 100644 index 0000000..861b2b2 --- /dev/null +++ b/q2_composition/_da_barplot/src/lib/SelectedTaxon.svelte @@ -0,0 +1,147 @@ + + + +
+ + +
+ {#if searchError != ""} +
+

{searchError}

+
+ {/if} +
+ + +
+
+ {#if taxonomyPlot?.selectedTaxon == undefined} + {#if searchError == ""} +

Click on a taxon name for more information.

+ {/if} + {:else} +

Name: {name}

+

+ Features classified to taxon: + {featureCount} ({featurePercent}%) +

+

+ Features classified to subtree: + {subtreeCount} ({subtreePercent}%) +

+ {/if} + + + diff --git a/q2_composition/_da_barplot/src/lib/Taxonomy.svelte b/q2_composition/_da_barplot/src/lib/Taxonomy.svelte new file mode 100644 index 0000000..2ee9f09 --- /dev/null +++ b/q2_composition/_da_barplot/src/lib/Taxonomy.svelte @@ -0,0 +1,37 @@ + + +
+
+ +
+ +
+ + diff --git a/q2_composition/_da_barplot/src/lib/TaxonomyFilter.svelte b/q2_composition/_da_barplot/src/lib/TaxonomyFilter.svelte new file mode 100644 index 0000000..d8a5806 --- /dev/null +++ b/q2_composition/_da_barplot/src/lib/TaxonomyFilter.svelte @@ -0,0 +1,99 @@ + + + +
+
+ + +
+
+ + +
+ +
+ + {#if errorMessage != ""} +
+

{errorMessage}

+
+ {/if} + + + diff --git a/q2_composition/_da_barplot/src/lib/TaxonomyFilterList.svelte b/q2_composition/_da_barplot/src/lib/TaxonomyFilterList.svelte new file mode 100644 index 0000000..96f072b --- /dev/null +++ b/q2_composition/_da_barplot/src/lib/TaxonomyFilterList.svelte @@ -0,0 +1,137 @@ + + + +
+ + +
+
+ + +
+
+ + +
+
+ {#each taxonomyFilters?.filters as filter} +
+ {#if filter.type == "feature-count"} +

features {"<"} {filter.value}

+ + {:else if filter.type == "individual"} +

+ individual filter of + {filter.node.getNonAnonymousTaxonString()} +

+ + {/if} +
+ {/each} +
+ diff --git a/q2_composition/_da_barplot/src/main.ts b/q2_composition/_da_barplot/src/main.ts new file mode 100644 index 0000000..664a057 --- /dev/null +++ b/q2_composition/_da_barplot/src/main.ts @@ -0,0 +1,9 @@ +import { mount } from 'svelte' +import './app.css' +import App from './App.svelte' + +const app = mount(App, { + target: document.getElementById('app')!, +}) + +export default app diff --git a/q2_composition/_da_barplot/src/util/features.svelte.ts b/q2_composition/_da_barplot/src/util/features.svelte.ts new file mode 100644 index 0000000..b5b85a5 --- /dev/null +++ b/q2_composition/_da_barplot/src/util/features.svelte.ts @@ -0,0 +1,309 @@ +import { TaxonomyNode } from "./taxonomy.svelte"; + +export type VariableRecord = { + name: string; + lfc?: number; + p?: number; + q?: number; + se?: number; + level?: string; + reference?: string; +} & Record; + +export class FeatureRecord { + featureId: string; + classification?: string; + shortClassification?: string; + variables: Map = new Map(); + + constructor(featureId: string, taxonomyNode?: TaxonomyNode) { + this.featureId = featureId; + + this.classification = taxonomyNode?.getFullTaxonString(); + if (taxonomyNode) { + const nonAnonymousName = taxonomyNode.getNonAnonymousTaxonString(); + this.shortClassification = `(${featureId.slice(0, 6)}) ${nonAnonymousName}`; + } + } + + /** + * Returns the variable with `variableName` and `level` or undefined if + * none is found. + */ + getVariable( + variableName: string, + level: string | undefined = undefined, + ): VariableRecord | undefined { + if (level) { + return this.variables.get(`${variableName}::${level}`); + } + + return this.variables.get(variableName); + } + + /** + * Creates a VariableRecord from primitives. + */ + createVariable( + variableName: string, + slice: string, + value: number, + level: string | undefined = undefined, + reference: string | undefined = undefined, + ): VariableRecord { + let variable = { + name: variableName, + [slice]: value, + }; + if (level && reference) { + variable.level = level; + variable.reference = reference; + } + + return variable; + } + + /** + * Adds a new variable to the set of feature variables. If a matching + * variable is already present then updates that variable with the any new + * slice properties from `variable`. + */ + addVariable(variable: VariableRecord): undefined { + let matchingVariable = this.getVariable(variable.name, variable.level); + + let newVariable: VariableRecord; + if (!matchingVariable) { + newVariable = variable; + } else { + newVariable = { + ...matchingVariable, + ...variable, + }; + } + + if (newVariable.level) { + this.variables.set( + `${newVariable.name}::${newVariable.level}`, + newVariable, + ); + } else { + this.variables.set(newVariable.name, newVariable); + } + } + + /** + * Returns the slice value for some variable. Errors if the variable or + * slice is not found. + */ + getVariableSlice( + variableName: string, + slice: string, + level: string | undefined = undefined, + ): number { + const variable = this.getVariable(variableName, level); + + if (!variable) { + throw new Error(`The ${variable} variable was not found.`); + } + if (!Object.hasOwn(variable, slice)) { + throw new Error(`The ${variable} variable has no ${slice} slice.`); + } + + return variable[slice] as number; + } +} + +export type ViewRecord = { + featureId: string; + lfc: number; + se: number; + p: number; + q: number; + classification: string; + shortClassification: string; +}; + +type Filter = { + (record: FeatureRecord): boolean; + slice: string; + relationship: string; + value: number; +}; + +export class FeatureRecords { + records: FeatureRecord[] = []; + + rootTaxon: TaxonomyNode | null = null; + hideFiltered: boolean = false; + showOnlyKept: boolean = false; + + view: ViewRecord[] = []; + viewVariable: string = $state(""); + viewVariableLevel: string = $state(""); + + filters: Filter[] = []; + + /** + * Returns an arbitrary variable record, useful for initializing the + * barplot. + */ + getInitialVariable(): VariableRecord { + return this.getAllVariables()[0]; + } + + /* + * Return the feature with id `featureId`, or undefined if not found. + */ + getFeature(featureId: string): FeatureRecord | undefined { + return this.records.find((r) => r.featureId == featureId); + } + + /** + * Adds a new feature. If a matching feature is already present then + * merges that feature's variables with those from `feature`. + */ + addFeature(feature: FeatureRecord): undefined { + let matchingFeature = this.getFeature(feature.featureId); + + if (!matchingFeature) { + this.records.push(feature); + } else { + Array.from(feature.variables.values()).forEach((v) => + matchingFeature.addVariable(v), + ); + } + } + + /** + * Adds a user-specified filter to the set of filters applied to the + * data. The filter function is annotated with each of this functions + * arguments for display in the UI. + */ + addFilter(slice: string, relationship: string, value: number) { + const filter = (record: FeatureRecord) => { + const variableValue = record.getVariableSlice( + this.viewVariable, + slice, + this.viewVariableLevel, + ); + + if (relationship == "gt") return variableValue > value; + if (relationship == "lt") return variableValue < value; + if (relationship == 'gtabsval') return Math.abs(variableValue) > value; + if (relationship == 'ltabsval') return Math.abs(variableValue) < value; + + throw new Error(`Unexpected relationship ${relationship}.`); + }; + + // annotate function with its defining characteristics + filter.slice = slice; + filter.relationship = relationship; + filter.value = value; + + this.filters.push(filter); + } + + /** + * Removes a filter by index. + */ + removeFilter(slice: string, relationship: string, value: number) { + this.filters = this.filters.filter((f) => { + return !( + f.slice == slice && + f.relationship == relationship && + f.value == value + ); + }); + } + + /** + * Returns all variable records in the feature dataset. Accessing only the + * first feature record is sufficient because all features have the same + * set of variable records. Removes the intercept variable record. + */ + getAllVariables(): VariableRecord[] { + const variables = Array.from(this.records[0].variables.values()); + return variables.filter((v) => v.name != "(Intercept)"); + } + + /** + */ + getVariablesWithName(variableName: string): VariableRecord[] { + const variables = this.getAllVariables(); + return variables.filter((v) => v.name == variableName); + } + + /** + * Renders the `view` by applying all existing filters, sorting features + * by decreasing lfc value, and extracting the slice values for the current + * `viewVariable`. + */ + render() { + let filtered: FeatureRecord[] = []; + + // apply taxonomyFilters if present + if (this.hideFiltered || this.showOnlyKept) { + for (let record of this.records) { + const node = this.rootTaxon.findTaxonById(record.featureId); + if (node == null) { + throw new Error( + `Could not find taxon with id ${record.featureId}`, + ); + } + + if (this.hideFiltered && !node.filtered) { + filtered.push(record); + } else if (this.showOnlyKept && node.hierarchyNode.keep) { + filtered.push(record); + } + } + } else { + filtered = this.records; + } + + // apply slice filters + for (let f of Object.values(this.filters)) { + filtered = filtered.filter(f); + } + + // map to view records by only selecting from variable of interest + let viewRecords: ViewRecord[] = filtered.map((record) => { + const variable = record.getVariable( + this.viewVariable, + this.viewVariableLevel, + ); + + if (!variable) { + throw new Error( + `Could not find variable ${this.viewVariable}.`, + ); + } + + let classification = record.classification; + if (classification == null) classification = "N/A"; + + return { + featureId: record.featureId, + lfc: variable.lfc!, + se: variable.se!, + p: variable.p!, + q: variable.q!, + classification, + shortClassification: record.shortClassification, + }; + }); + + // filter null lfc values + viewRecords = viewRecords.filter((r) => r.lfc != null); + + // sort view records by decreasing lfc + viewRecords = viewRecords.sort((r1, r2) => r2.lfc - r1.lfc); + + // update state + this.view = viewRecords; + } +} + +// global state +let features = new FeatureRecords(); +export default features; diff --git a/q2_composition/_da_barplot/src/util/parse.ts b/q2_composition/_da_barplot/src/util/parse.ts new file mode 100644 index 0000000..cfbc06b --- /dev/null +++ b/q2_composition/_da_barplot/src/util/parse.ts @@ -0,0 +1,148 @@ +import { text } from "d3-fetch"; + +import { + FeatureRecords, + FeatureRecord, + type VariableRecord, +} from "./features.svelte"; + +import { TaxonomyNode } from "./taxonomy.svelte"; + +type JSONLHeaderField = { + name: string; + type: string | null; + missing: boolean; + title: string; + description: string; + extra: Record; +}; +type JSONLHeader = { + doctype: object; + direction: string; + style: string; + fields: JSONLHeaderField[]; +}; +type JSONLFeatureRecord = { + taxon: string; +} & Record; + +/** + * Parses slice data from the ANCOMBC2 output format that resides inside of the + * visualization artifact. Side-effects `featureRecords` by adding/updating + * parsed features. + */ +export async function parseAllSlices( + slicesDir: string, + featureRecords: FeatureRecords, + rootTaxon: TaxonomyNode | null = null, +): Promise { + const slices = ["lfc", "p", "q", "se"]; + for (let slice of slices) { + const sliceFilepath = `${slicesDir}/${slice}.jsonl`; + await parseSlice(sliceFilepath, featureRecords, rootTaxon); + } + + return Promise.resolve(); +} + +/** + * Parses a JSONL slice into `FeatureRecord`s and adds them to `featureRecords`. + */ +export async function parseSlice( + sliceFilepath: string, + featureRecords: FeatureRecords, + rootTaxon: TaxonomyNode | null, +): Promise { + // open file, convert to json + const textData: string = await text(sliceFilepath); + const jsonRecords: any = textData + .split("\n") + .filter((line) => line.trim() != "") + .map((line) => JSON.parse(line)); + + // parse header and check if empty + if (jsonRecords.length < 1) { + const msg = `The ${sliceFilepath} slice is empty.`; + throw new Error(msg); + } else if (jsonRecords.length === 1) { + const msg = `The ${sliceFilepath} slice has a header but no records.`; + throw new Error(msg); + } + const header: JSONLHeader = jsonRecords.shift()!; + + // parse each remaining line into a feature record + const jsonFeatureRecords: JSONLFeatureRecord[] = jsonRecords; + const sliceName = sliceFilepath.split("/").pop()!.replace(".jsonl", ""); + + jsonFeatureRecords.forEach((record) => { + const feature = parseJSONLFeatureRecord( + record, + header, + sliceName, + rootTaxon, + ); + featureRecords.addFeature(feature); + }); +} + +/** + * Parses a feature record line from a JSONL slice into a `FeatureRecord` + * object. + */ +export function parseJSONLFeatureRecord( + jsonRecord: JSONLFeatureRecord, + header: JSONLHeader, + slice: string, + rootTaxon: TaxonomyNode | null, +): FeatureRecord { + const taxonNode = rootTaxon?.findTaxonById(jsonRecord.taxon); + + const featureRecord = new FeatureRecord(jsonRecord.taxon, taxonNode); + + for (let column of Object.keys(jsonRecord)) { + if (column == "taxon") continue; + + const value = jsonRecord[column]; + + const headerField = getColumnField(column, header); + + let variable: VariableRecord; + if (headerField.extra.reference) { + variable = featureRecord.createVariable( + headerField.extra.variable, + slice, + value, + headerField.extra.level, + headerField.extra.reference, + ); + } else { + variable = featureRecord.createVariable(column, slice, value); + } + + featureRecord.addVariable(variable); + } + + return featureRecord; +} + +/** + * Retrieves the header field entry for the `column` column. + */ +export function getColumnField( + column: string, + header: JSONLHeader, +): JSONLHeaderField { + const columnFields: JSONLHeaderField[] = header.fields.filter((field) => { + return field.name === column; + }); + + if (columnFields.length > 1) { + const msg = `Duplicate name '${column}' found in JSONL header.`; + throw new Error(msg); + } else if (!columnFields.length) { + const msg = `Column ${column} not found in JSONL header.`; + throw new Error(msg); + } + + return columnFields.shift()!; +} diff --git a/q2_composition/_da_barplot/src/util/plot.ts b/q2_composition/_da_barplot/src/util/plot.ts new file mode 100644 index 0000000..ef3a2e5 --- /dev/null +++ b/q2_composition/_da_barplot/src/util/plot.ts @@ -0,0 +1,526 @@ +import * as d3 from "d3"; +import { type ViewRecord } from "./features.svelte"; + +type PlotDimensions = { + svgWidth: number; + svgHeight: number; + margin: number; + plotWidth: number; + plotHeight: number; + barHeight: number; + barPadding: number; +}; + +export class DivergingBarplot { + data: ViewRecord[] = []; + dimensions: PlotDimensions = {}; + xScale: d3.ScaleLinear = d3.scaleLinear(); + yScale: d3.ScaleBand = d3.scaleBand(); + xAxis: d3.Selection = d3.selection(); + yAxis: d3.Selection = d3.selection(); + + /** + */ + init(data: ViewRecord[]) { + this.data = data; + this.dimensions = this.createDimensions(); + this.xScale = this.createXScale(); + this.yScale = this.createYScale(); + this.xAxis = this.createXAxis(); + this.yAxis = this.createYAxis(); + } + + /** + */ + createDimensions(): PlotDimensions { + const svg = d3.select("svg"); + let svgWidth: number; + if (!svg.empty()) { + svgWidth = svg.node()!.getBoundingClientRect().width; + } else { + throw new Error(`Svg element not found.`); + } + + const numFeatures = this.data.length; + + const barHeight = 20; + const barPadding = 1.25; + + const plotHeight = numFeatures * barHeight * barPadding; + + const margin = 120; + const plotWidth = svgWidth - 2 * margin; + + return { + svgWidth: svgWidth, + svgHeight: plotHeight + 2 * margin, + margin, + plotWidth, + plotHeight, + barHeight, + barPadding, + }; + } + + /** + * Updates the plotted data and redraws the plot if the data is non-empty, + * otherwise hides the plot. + */ + updateData(data: ViewRecord[]) { + this.data = data; + if (data.length > 0) { + this.showPlot(); + this.drawPlot(true); + } else { + this.hidePlot(); + } + } + + /** + */ + updatePlotHeight() { + this.dimensions.plotHeight = + this.data.length * + this.dimensions.barHeight * + this.dimensions.barPadding; + this.dimensions.svgHeight = + this.dimensions.plotHeight + 2 * this.dimensions.margin; + } + + /** + */ + increaseBarThickness() { + this.dimensions.barHeight *= 1.1; + this.drawPlot(true); + } + + /** + */ + decreaseBarThickness() { + this.dimensions.barHeight *= 0.9; + this.drawPlot(true); + } + + /** + */ + getXDomain(): [number, number] { + // get min and max lfc +- se values + const lfc_minus_se = this.data.map((f) => f.lfc - f.se); + const lfc_plus_se = this.data.map((f) => f.lfc + f.se); + + let [min, max] = d3.extent([...lfc_minus_se, ...lfc_plus_se]); + + if (min == undefined || max == undefined) { + throw new Error("Unable to find min/max of feature lfcs."); + } + + // calculate scale range + const scaleMargin = 0.25; + if (min < 0) { + min = (1 + scaleMargin) * min; + } else { + min = -scaleMargin * max; + } + + if (max > 0) { + max = (1 + scaleMargin) * max; + } else { + max = -scaleMargin * min; + } + + return [min, max]; + } + + /** + */ + getXRange() { + return [ + this.dimensions.margin, + this.dimensions.margin + this.dimensions.plotWidth, + ]; + } + + /** + */ + createXScale(): d3.ScaleLinear { + const domain = this.getXDomain(); + const range = this.getXRange(); + const scale = d3.scaleLinear().domain(domain).range(range); + + return scale; + } + + /** + */ + getYDomain(): string[] { + return d3.range(0, this.data.length).map((i) => String(i)); + } + + /** + */ + getYRange() { + return [ + this.dimensions.margin, + this.dimensions.margin + this.dimensions.plotHeight, + ]; + } + + /** + */ + createYScale(): d3.ScaleBand { + const domain = this.getYDomain(); + const range = this.getYRange(); + const scale = d3.scaleBand().domain(domain).range(range); + + return scale; + } + + /** + */ + getXAxisTranslation() { + const translation = this.dimensions.margin + this.dimensions.plotHeight; + return `translate(0, ${translation})`; + } + + /** + */ + getYAxisTranslation() { + return `translate(${this.xScale(0)}, 0)`; + } + + /** + */ + createXAxis(): d3.Selection { + let axis = d3 + .select("svg") + .append("g") + .attr("class", "x-axis") + .attr("transform", this.getXAxisTranslation()) + .call(d3.axisBottom(this.xScale)); + + axis.selectAll("text").attr("font-size", "14px"); + + axis.append("text") + .text("LFC (Log Fold Change)") + .attr("fill", "black") + .attr("font-size", "18px") + .attr("id", "xaxis-label") + .attr("x", "50%") + .attr("y", 60); + + return axis; + } + + /** + */ + createYAxis(): d3.Selection { + let axis = d3 + .select("svg") + .append("g") + .attr("class", "y-axis") + .attr("transform", this.getYAxisTranslation()) + .call( + d3 + .axisLeft(this.yScale) + .tickSize(0) + .tickFormat("" as any), + ); + + return axis; + } + + /** + */ + addHoverHandlers() { + // event handlers + const handleMouseover = (e: any, d: any) => { + const tooltipData = [ + `feature ID: ${d.featureId}`, + `classification: ${d.classification}`, + `lfc: ${d.lfc}`, + `se: ${d.se}`, + `p-value: ${d.p}`, + `q-value: ${d.q}`, + ]; + + d3.select(".tooltip") + .style("display", "unset") + .style("left", `${e.clientX + 25}px`) + .style("top", `${e.clientY - 10}px`) + .selectAll("p") + .data(tooltipData) + .join("p") + .text((d, i) => tooltipData[i]) + .style("margin", "2px") + .style("box-shadow", "none"); + + d3.select(".tooltip") + .transition() + .duration(200) + .style("opacity", 1); + }; + + const handleMousemove = (e: any, d: any) => { + d3.select(".tooltip") + .style("left", `${e.clientX + 25}px`) + .style("top", `${e.clientY - 10}px`); + }; + + const handleMouseout = (e: any, d: any) => { + d3.select(".tooltip") + .transition() + .duration(200) + .style("opacity", 0) + .end() + .then(() => { + d3.select(".tooltip").style("display", "none"); + }); + }; + + // create tooltip + d3.select("body") + .selectAll(".tooltip") + .data([1]) + .join("div") + .attr("class", "tooltip") + .style("background-color", "#f0edef") + .style("padding", "10px") + .style("border-radius", "10px") + .style("position", "absolute") + .style("box-shadow", "1px 1px 2px gray") + .style("display", "none") + .style("opacity", 0); + + // register event handlers + d3.select("svg") + .selectAll("rect, .error-bar") + .on("mouseover", handleMouseover) + .on("mousemove", handleMousemove) + .on("mouseout", handleMouseout); + } + + /** + */ + drawErrorBar(path: d3.Path, d: ViewRecord, i: number): d3.Path { + // calculate error bar layout + const startX = this.xScale(d.lfc)!; + const startY = + this.yScale(i.toString())! + this.dimensions.barHeight / 2; + + const errorBarRight = this.xScale(d.lfc + d.se); + const errorBarLeft = startX - (errorBarRight - startX); + const errorBarTop = startY + 0.25 * this.dimensions.barHeight; + const errorBarBottom = startY - 0.25 * this.dimensions.barHeight; + + // draw error bar + path.moveTo(errorBarRight, errorBarTop); + path.lineTo(errorBarRight, errorBarBottom); + path.moveTo(errorBarRight, startY); + path.lineTo(errorBarLeft, startY); + path.moveTo(errorBarLeft, errorBarTop); + path.lineTo(errorBarLeft, errorBarBottom); + + return path; + } + + /** + */ + drawPlot(transition: boolean) { + const sizeSvg = () => { + let svg = d3 + .select("svg") + .attr("width", this.dimensions.svgWidth) + .attr("height", this.dimensions.svgHeight); + }; + + if (!transition) { + sizeSvg(); + } + + if (transition) { + // update plot height + this.updatePlotHeight(); + + // update scales + const xDomain = this.getXDomain(); + const xRange = this.getXRange(); + const yDomain = this.getYDomain(); + const yRange = this.getYRange(); + + this.xScale.domain(xDomain).range(xRange); + this.yScale.domain(yDomain).range(yRange); + + // resize svg + sizeSvg(); + + // transition axes + this.xAxis + .transition() + .duration(500) + .attr("transform", this.getXAxisTranslation()) + .call(d3.axisBottom(this.xScale)); + + this.xAxis.selectAll("text").attr("font-size", "14px"); + this.xAxis.select("#xaxis-label").attr("font-size", "18px"); + + this.yAxis + .transition() + .duration(500) + .attr("transform", this.getYAxisTranslation()) + .call( + d3 + .axisLeft(this.yScale) + .tickSize(0) + .tickFormat("" as any), + ); + } + + // draw bars + let barSelection = d3 + .select("svg") + .selectAll("rect") + .data(this.data) + .join("rect"); + + const drawBars = (selection: any) => { + selection + .attr("x", (d) => + d.lfc > 0 ? this.xScale(0) : this.xScale(d.lfc), + ) + .attr("y", (d, i) => this.yScale(String(i))) + .attr("width", (d) => + Math.abs(this.xScale(d.lfc) - this.xScale(0)), + ) + .attr("height", this.dimensions.barHeight) + .attr("fill", (d) => (d.lfc > 0 ? "green" : "red")); + }; + + if (transition) { + barSelection.transition().duration(400).call(drawBars.bind(this)); + } else { + barSelection.call(drawBars.bind(this)); + } + + // draw error bars + let errorBarSelection = d3 + .select("svg") + .selectAll(".error-bar") + .data(this.data) + .join("path") + .attr("class", "error-bar"); + + const drawErrorBars = (selection: any) => { + selection + .attr("d", (d, i) => + this.drawErrorBar(d3.path(), d, i).toString(), + ) + .attr("stroke", "black") + .attr("stroke-width", "2px"); + }; + + if (transition) { + errorBarSelection + .transition() + .duration(400) + .call(drawErrorBars.bind(this)); + } else { + errorBarSelection.call(drawErrorBars.bind(this)); + } + + // draw labels + let labelSelection = d3 + .select("svg") + .selectAll(".label") + .data(this.data) + .join("text") + .attr("class", "label"); + + const drawLabels = (selection: any) => { + selection + .text((d) => { + let classification = d.shortClassification + ? d.shortClassification + : d.featureId; + + if (classification.length > 30) { + classification = classification.slice(0, 25) + "(...)"; + } + + return classification; + }) + .attr("x", (d) => { + if (d.lfc > 0) { + return Math.min( + this.xScale(d.lfc - d.se), + this.xScale(0), + ); + } + return Math.max(this.xScale(d.lfc + d.se), this.xScale(0)); + }) + .attr( + "y", + (d, i) => + this.yScale(String(i)) + this.yScale.bandwidth() / 2, + ) + .attr("text-anchor", (d) => (d.lfc > 0 ? "end" : "start")) + .attr("dx", (d) => (d.lfc > 0 ? -8 : 8)) + .attr("dy", "1px") + .attr("font-size", "12px") + .attr("fill", "#474747"); + }; + + if (transition) { + labelSelection + .transition() + .duration(400) + .call(drawLabels.bind(this)); + } else { + labelSelection.call(drawLabels.bind(this)); + } + + // attach hover event listeners + this.addHoverHandlers(); + } + + /** + */ + hidePlot() { + // gray-out the plot + d3.select("svg") + .append("rect") + .attr("class", "hider") + .attr("width", this.dimensions.svgWidth) + .attr("height", this.dimensions.svgHeight) + .attr("fill", "gray") + .attr("opacity", 0.9); + + // add error message + d3.select("svg") + .append("rect") + .attr("class", "hider-text-box") + .attr("x", 0.3 * this.dimensions.svgWidth) + .attr("y", 0.4 * this.dimensions.svgHeight) + .attr("width", 0.4 * this.dimensions.svgWidth) + .attr("height", 0.2 * this.dimensions.svgHeight) + .attr("fill", "white"); + + d3.select("svg") + .append("text") + .attr("class", "hider-text") + .text("Oops! All features were filtered.") + .attr("x", this.dimensions.svgWidth / 2) + .attr("y", this.dimensions.svgHeight / 2) + .attr("dominant-baseline", "middle") + .attr("text-anchor", "middle") + .attr("font-size", "18px"); + } + + /** + */ + showPlot() { + d3.selectAll(".hider, .hider-text, .hider-text-box").remove(); + } +} + +const plot = new DivergingBarplot(); +export default plot; diff --git a/q2_composition/_da_barplot/src/util/taxonomy.svelte.ts b/q2_composition/_da_barplot/src/util/taxonomy.svelte.ts new file mode 100644 index 0000000..d362f6d --- /dev/null +++ b/q2_composition/_da_barplot/src/util/taxonomy.svelte.ts @@ -0,0 +1,729 @@ +import { tsv } from "d3-fetch"; +import * as d3 from "d3"; + +type PlotDimensions = { + margin: number; + nodeWidth: number; + nodeHeight: number; + boxHeight: number; + boxWidth: number; +}; + +export class TaxonomyPlot { + dimensions: PlotDimensions; + root: d3.HierarchyNode; + treeLayout: d3.TreeLayout; + link: d3.Link; + + selectedTaxon: TaxonomyNode | null = $state(null); + hideFiltered: boolean = false; + + constructor(root: d3.HierarchyNode) { + this.root = root; + this.initTree(this.root); + + this.dimensions = this.getDimensions(); + this.treeLayout = this.createTreeLayout(); + this.link = this.createLinkGenerator(); + + this.initSvg(); + } + + initTree(root: d3.HierarchyNode) { + root.descendants().forEach((node, i) => { + node._children = node.children; + node.id = i; + node.children = null; + node.expand = false; + node.keep = false; + node.match = false; + }); + } + + getSvgDimensions() { + const svg = d3.select("#taxonomy-svg-container svg"); + + if (svg.empty()) { + throw new Error("No svg element found."); + } + + const svgRect = (svg.node() as any).getBoundingClientRect(); + + return { width: svgRect.width, height: svgRect.height }; + } + + getDimensions() { + const margin = 25; + + const { width: svgWidth, height: svgHeight } = this.getSvgDimensions(); + + const taxonomyDepth = this.root.height; + const nodeWidth = 225; + const nodeHeight = 30; + + const dimensions: PlotDimensions = { + margin: margin, + nodeHeight: nodeHeight, + nodeWidth: nodeWidth, + boxWidth: 0.8 * nodeWidth, + boxHeight: 0.8 * nodeHeight, + }; + + return dimensions; + } + + createTreeLayout(): d3.TreeLayout { + const treeLayout = d3 + .tree() + .nodeSize([this.dimensions.nodeHeight, this.dimensions.nodeWidth]); + + return treeLayout; + } + + createLinkGenerator(): d3.Link { + return d3 + .linkHorizontal() + .x((d) => d.y) + .y((d) => d.x); + } + + initSvg() { + const svg = d3.select("#taxonomy-svg-container svg"); + + // create groups for nodes and links + const zoomContainer = svg.append("g"); + zoomContainer.append("g").attr("class", "link-group"); + zoomContainer.append("g").attr("class", "node-group"); + + // set svg view box + const { width: svgWidth, height: svgHeight } = this.getSvgDimensions(); + + svg.attr("viewBox", [ + -this.dimensions.margin, + -svgHeight / 2, + svgWidth, + svgHeight, + ]); + + // make svg zoomable & pannable + const zoom = d3 + .zoom() + .scaleExtent([0.4, 2]) + .on("zoom", (event) => { + zoomContainer.attr("transform", event.transform); + }); + + svg.call(zoom).on("dblclick.zoom", null); + } + + addSelectHandlers() { + d3.selectAll(".taxonomy-node").on("click", (event, d) => { + this.selectedTaxon = d.data; + }); + } + + addExpandHandlers() { + d3.selectAll(".expand-button").on("click", (event, d) => { + d.expand = !d.expand; + this.render(d); + + event.stopPropagation(); + }); + } + + addKeepHandlers() { + d3.selectAll(".keep-button").on("click", (event, d) => { + d.keep = !d.keep; + + const fillColor = d.keep ? "orange" : "lightgray"; + d3.select(event.currentTarget) + .select("rect") + .attr("fill", fillColor); + + this.render(d); + + event.stopPropagation(); + }); + } + + drawButton( + selection: d3.Selection, + type: "expand" | "keep", + ) { + let xTranslation; + let className; + let letter; + if (type == "expand") { + xTranslation = this.dimensions.boxWidth - this.dimensions.boxHeight; + className = "expand-button"; + letter = "E"; + } else if (type == "keep") { + xTranslation = + this.dimensions.boxWidth - 2 * this.dimensions.boxHeight; + className = "keep-button"; + letter = "K"; + } else { + throw new Error("Unrecognized button type."); + } + + const button = selection + .append("g") + .attr("class", className) + .attr("transform", `translate(${xTranslation}, 2)`); + + button + .append("rect") + .attr("width", this.dimensions.boxHeight - 4) + .attr("height", this.dimensions.boxHeight - 4) + .attr("fill", "lightgray"); + + if (type == "keep") { + button + .selectAll("rect") + .attr("fill", (d) => (d.keep ? "orange" : "lightgray")); + } + + button + .append("text") + .text(letter) + .attr("x", this.dimensions.boxHeight / 2 - 2) + .attr("y", this.dimensions.boxHeight / 2 - 2) + .attr("dominant-baseline", "middle") + .attr("text-anchor", "middle") + .attr("font-size", 14) + .attr("dy", 2); + } + + drawNodes( + nodes: d3.HierarchyNode[], + source: d3.HierarchyNode, + ) { + const updateSelection = d3 + .select(".node-group") + .selectAll(".taxonomy-node") + .data(nodes, (d) => d.id); + + // create entering node groups + const enterSelection = updateSelection + .enter() + .append("g") + .attr("class", "taxonomy-node") + .attr("cursor", "pointer") + .attr("transform", (d) => `translate(${source.y0}, ${source.x0})`) + .attr("stroke-opacity", 1) + .attr("fill-opacity", 1); + + // taxon names + enterSelection + .append("text") + .text((d) => { + if (d.data.name.length > 18) { + return d.data.name.slice(0, 15) + "..."; + } + return d.data.name; + }) + .attr("dx", 10) + .attr("y", this.dimensions.boxHeight / 2) + .attr("dominant-baseline", "middle") + .attr("stroke-linejoin", "round") + .attr("stroke-width", 5) + .attr("stroke", "white") + .attr("paint-order", "stroke") + .attr("font-weight", "bold") + .attr("font-size", 13); + + // draw taxon boxes + enterSelection + .append("rect") + .attr("class", "taxon-box") + .attr("height", this.dimensions.boxHeight) + .attr("width", this.dimensions.boxWidth) + .attr("fill", (d) => { + if (d.data.searchMatch) return "green"; + if (d.data.filtered) return "red"; + return "white"; + }) + .attr("stroke", "gray") + .attr("stroke-width", 2) + .attr("rx", 2) + .attr("ry", 2) + .attr("stroke-opacity", 1) + .attr("fill-opacity", (d) => { + if (d.data.searchMatch || d.data.filtered) { + return 0.2; + } + return 0; + }); + + // left circle + enterSelection + .append("circle") + .attr("cx", 0) + .attr("cy", this.dimensions.boxHeight / 2) + .attr("r", 3) + .attr("fill", "#555"); + + // right circle; visible only if node has children + enterSelection + .append("circle") + .attr("class", "right-circle") + .attr("cx", this.dimensions.boxWidth) + .attr("cy", this.dimensions.boxHeight / 2) + .attr("r", (d) => { + let kept = d._children; + if (this.hideFiltered) { + kept = d._children?.filter((n) => !n.data.filtered); + } + if (kept && kept.length > 0) { + return 3; + } + return 0; + }) + .attr("fill", "#555"); + + updateSelection.selectAll(".right-circle").attr("r", (d) => { + let kept = d._children; + if (this.hideFiltered) { + kept = d._children?.filter((n) => !n.data.filtered); + } + if (kept && kept.length > 0) { + return 3; + } + return 0; + }); + + // color search matches + updateSelection + .selectAll(".taxon-box") + .attr("fill", (d) => { + if (d.data.searchMatch) return "green"; + if (d.data.filtered) return "red"; + return "white"; + }) + .attr("fill-opacity", (d) => { + if (d.data.searchMatch || d.data.filtered) { + return 0.2; + } + return 0; + }); + + this.drawButton(enterSelection, "expand"); + this.drawButton(enterSelection, "keep"); + + // add click event handlers + this.addSelectHandlers(); + this.addExpandHandlers(); + this.addKeepHandlers(); + + // color buttons + updateSelection + .merge(enterSelection) + .selectAll(".expand-button") + .select("rect") + .attr("fill", (d) => { + if (d.children && d.children.length == d._children.length) { + return "lightblue"; + } else { + return "lightgray"; + } + }); + + updateSelection + .merge(enterSelection) + .selectAll(".keep-button") + .select("rect") + .attr("fill", (d) => (d.keep ? "orange" : "lightgray")); + + // transition all nodes to their new positions + updateSelection + .merge(enterSelection) + .transition() + .duration(200) + .attr("transform", (d) => `translate(${d.y}, ${d.x})`) + .attr("fill-opacity", 1) + .attr("stroke-opacity", 1); + + // transition exiting nodes to parents' new positions + updateSelection + .exit() + .transition() + .duration(200) + .remove() + .attr("transform", (d) => `translate(${source.y}, ${source.x})`) + .attr("fill-opacity", 0) + .attr("stroke-opacity", 0); + } + + drawLinks( + links: d3.HierarchyLink[], + source: d3.HierarchyNode, + ) { + const updateSelection = d3 + .select(".link-group") + .selectAll(".taxonomy-link") + .data(links, (d) => d.target.id); + + // create entering link paths + const enterSelection = updateSelection + .enter() + .append("path") + .attr("class", "taxonomy-link") + .attr("fill", "none") + .attr("stroke", "#555") + .attr("stroke-opacity", 0.5) + .attr("stroke-width", 1.5) + .attr("d", (d) => { + const parentOld = { x: source.x0, y: source.y0 }; + return this.link({ source: parentOld, target: parentOld }); + }); + + // transition all links to their new shapes + updateSelection + .merge(enterSelection) + .transition() + .duration(200) + .attr("d", (d) => { + const sourceX = d.source.x! + this.dimensions.boxHeight / 2; + const targetX = d.target.x! + this.dimensions.boxHeight / 2; + + const sourceY = d.source.y! + this.dimensions.boxWidth; + const targetY = d.target.y!; + + const positions = { + source: { x: sourceX, y: sourceY }, + target: { x: targetX, y: targetY }, + }; + return this.link(positions); + }); + + // transition exiting links to parent's new position + updateSelection + .exit() + .transition() + .duration(200) + .remove() + .attr("d", (d) => { + const parentNew = { x: source.x, y: source.y }; + return this.link({ source: parentNew, target: parentNew }); + }); + } + + assignChildren(node: d3.HierarchyNode): boolean { + let keptDescendant = node.keep || node.data.searchMatch; + + if (this.hideFiltered && node.data.filtered) { + return false; + } + + // leaf + if (!node._children) { + return keptDescendant; + } + + node.children = []; + for (let child of node._children) { + if (this.assignChildren(child)) { + node.children.push(child); + keptDescendant = true; + } + } + + if (node.expand) { + node.children = node._children; + if (this.hideFiltered) { + node.children = node.children.filter((n) => !n.data.filtered); + } + } + + if (node.children!.length == 0) { + node.children = undefined; + } + + return keptDescendant; + } + + render(source: d3.HierarchyNode) { + // update visible children + this.assignChildren(this.root); + + // gather all expanded nodes and links + const nodes = this.root.descendants().reverse(); + const links = this.root.links(); + + // assign coordinates to nodes + this.treeLayout(this.root); + + // const transition = this.resizeSvg(); + this.drawLinks(links, source); + this.drawNodes(nodes, source); + + // store the current positions for the next render + this.root.eachBefore((node) => { + node.x0 = node.x; + node.y0 = node.y; + }); + } +} + +export class TaxonomyNode { + name: string; + parent: TaxonomyNode | null; + children: TaxonomyNode[]; + featureIDs: string[]; + hierarchyNode: d3.HierarchyNode | null; + searchMatch: boolean = false; + filtered: boolean = false; + + constructor(name: string, parent: TaxonomyNode | null) { + this.name = name; + this.parent = parent; + this.children = []; + this.featureIDs = []; + this.hierarchyNode = null; + } + + getChild(name: string): TaxonomyNode | null { + let matchingChildren = this.children.filter((child) => { + return child.name == name; + }); + + if (matchingChildren.length > 1) { + throw new Error("More than one matching child found."); + } + if (matchingChildren.length == 0) { + return null; + } + + return matchingChildren[0]; + } + + getRoot(): TaxonomyNode { + let currentNode: TaxonomyNode = this; + while (currentNode.parent != null) { + currentNode = currentNode.parent; + } + + return currentNode; + } + + getDescendants(): TaxonomyNode[] { + const descendants: TaxonomyNode[] = [this]; + for (let child of this.children) { + descendants.push(...child.getDescendants()); + } + + return descendants; + } + + findTaxa(name: string): TaxonomyNode[] { + const root = this.getRoot(); + const descendants = root.getDescendants(); + + const matches = descendants.filter((descendant) => { + const index = descendant.name + .toLowerCase() + .indexOf(name.toLowerCase()); + + return index != -1 && !descendant.filtered; + }); + + return matches; + } + + findTaxonById(id: string): TaxonomyNode | null { + const descendants = this.getRoot().getDescendants(); + const matches = descendants.filter((descendant) => { + return descendant.featureIDs.indexOf(id) != -1; + }); + + if (matches.length == 0) { + return null; + } else if (matches.length == 1) { + return matches[0]; + } else { + throw new Error( + "More than one taxonomy node with the same feature ID.", + ); + } + } + + getAncestors(): TaxonomyNode[] { + const ancestors = []; + let currentNode: TaxonomyNode = this; + while (currentNode.parent != null) { + ancestors.push(currentNode); + currentNode = currentNode.parent; + } + + return ancestors; + } + + getFullTaxonString(): string { + const ancestorNames = this.getAncestors() + .reverse() + .map((a) => a.name); + + return ancestorNames.join(";"); + } + + /** + * Gets the shortest taxonomy string that contains a non-anonymous level + * label. + * + * Examples: + * (...);f__family;g__genus;s__ => g__genus;s__ + * (...);o__order;f__family;g__;s__ => f__family;g__;s__ + * (...);g__genus;s__species => s__species + */ + getNonAnonymousTaxonString(): string { + if (this.parent == null) return "root"; + + const ancestorNames = this.getAncestors() + .reverse() + .map((a) => a.name); + + let lastNonAnonymousIndex = null; + for (const [index, ancestorName] of ancestorNames.entries()) { + if (ancestorName.slice(-2) != "__") { + lastNonAnonymousIndex = index; + } + } + if (lastNonAnonymousIndex == null) lastNonAnonymousIndex = 0; + + return ancestorNames.slice(lastNonAnonymousIndex).join(";"); + } + + getFeatureCount(): number { + return this.featureIDs.length; + } + + getSubtreeFeatureCount(): number { + let subtreeCount = this.getFeatureCount(); + + for (let child of this.children) { + subtreeCount += child.getSubtreeFeatureCount(); + } + + return subtreeCount; + } + + getTreeFeatureCount(): number { + return this.getRoot().getSubtreeFeatureCount(); + } + + clearSearchMatches() { + this.getRoot() + .getDescendants() + .forEach((n) => { + n.searchMatch = false; + }); + } +} + +export class TaxonomyFilters { + filters: ((node: TaxonomyNode) => boolean)[] = $state([]); + taxonomyRoot: TaxonomyNode; + + constructor(taxonomyRoot: TaxonomyNode) { + this.filters = []; + this.taxonomyRoot = taxonomyRoot; + } + + addFeatureCountFilter(featureCount: number) { + const filter = (node: TaxonomyNode) => { + return node.getSubtreeFeatureCount() < featureCount; + }; + + filter.type = "feature-count"; + filter.value = featureCount; + + this.filters = [...this.filters, filter]; + } + + removeFeatureCountFilter(value: number) { + this.filters = this.filters.filter((f) => { + if (f.type != "feature-count") return true; + + return !(f.value == value); + }); + } + + addIndividualFilter(filterNode: TaxonomyNode) { + const filter = (node: TaxonomyNode) => { + return node == filterNode; + }; + + filter.type = "individual"; + filter.node = filterNode; + + this.filters = [...this.filters, filter]; + } + + removeIndividualFilter(filterNode: TaxonomyNode) { + this.filters = this.filters.filter((f) => { + if (f.type != "individual") return true; + + return !(f.node == filterNode); + }); + } + + applyFilters() { + const nodes = this.taxonomyRoot.getDescendants(); + + nodes.forEach((node) => (node.filtered = false)); + + nodes.forEach((node) => { + for (let filter of this.filters) { + node.filtered = filter(node); + if (node.filtered) return; + } + }); + } +} + +/** + * Parses a taxonomy.tsv file into a d3.hierarchy. + */ +export async function parseTaxonomy( + taxonomyFilepath: string, +): Promise> { + const taxonomyRecords = await tsv(taxonomyFilepath); + + const root = new TaxonomyNode("root", null); + + for (let taxonRecord of taxonomyRecords) { + const levelNames = taxonRecord["Taxon"] + .split(";") + .filter((n) => n != ""); + const featureId = taxonRecord["Feature ID"]; + + let parentNode = root; + for (let [levelIndex, levelName] of levelNames.entries()) { + const currentNode = new TaxonomyNode(levelName, parentNode); + + // if this is the last level then it has a feature ID + if (levelIndex == levelNames.length - 1) { + currentNode.featureIDs.push(featureId); + } + + // merge with matching child if one exists + const matchingChild = parentNode.getChild(levelName); + if (matchingChild) { + matchingChild.featureIDs.push(...currentNode.featureIDs); + parentNode = matchingChild; + } else { + parentNode.children.push(currentNode); + parentNode = currentNode; + } + } + } + + const hierarchyRoot = d3.hierarchy(root); + + // create back references from TaxonomyNodes to d3 nodes + hierarchyRoot.eachBefore((node) => { + node.data.hierarchyNode = node; + }); + + return hierarchyRoot; +} diff --git a/q2_composition/_da_barplot/src/vite-env.d.ts b/q2_composition/_da_barplot/src/vite-env.d.ts new file mode 100644 index 0000000..4078e74 --- /dev/null +++ b/q2_composition/_da_barplot/src/vite-env.d.ts @@ -0,0 +1,2 @@ +/// +/// diff --git a/q2_composition/_da_barplot/svelte.config.js b/q2_composition/_da_barplot/svelte.config.js new file mode 100644 index 0000000..b0683fd --- /dev/null +++ b/q2_composition/_da_barplot/svelte.config.js @@ -0,0 +1,7 @@ +import { vitePreprocess } from '@sveltejs/vite-plugin-svelte' + +export default { + // Consult https://svelte.dev/docs#compile-time-svelte-preprocess + // for more information about preprocessors + preprocess: vitePreprocess(), +} diff --git a/q2_composition/_da_barplot/tests/data/output-format/W.jsonl b/q2_composition/_da_barplot/tests/data/output-format/W.jsonl new file mode 100644 index 0000000..b2b60e3 --- /dev/null +++ b/q2_composition/_da_barplot/tests/data/output-format/W.jsonl @@ -0,0 +1,9 @@ +{"doctype":{"name":"table.jsonl","format":"application/x-json-lines","version":"1.0"},"direction":"row","style":"key:value","fields":[{"name":"taxon","type":null,"missing":false,"title":"","description":"","extra":{}},{"name":"(Intercept)","type":null,"missing":false,"title":"","description":"","extra":{}},{"name":"body-site::left palm","type":null,"missing":false,"title":"","description":"","extra":{"variable":"body-site","level":"left palm","reference":"gut"}},{"name":"body-site::right palm","type":null,"missing":false,"title":"","description":"","extra":{"variable":"body-site","level":"right palm","reference":"gut"}},{"name":"body-site::tongue","type":null,"missing":false,"title":"","description":"","extra":{"variable":"body-site","level":"tongue","reference":"gut"}},{"name":"year","type":null,"missing":false,"title":"","description":"","extra":{}}],"index":[],"title":"","description":"","extra":{}} +{"taxon":"4b5eeb300368260019c1fbc7a3c718fc","(Intercept)":-1235411664.1230688095,"body-site::left palm":15.5292100831,"body-site::right palm":10.7105143567,"body-site::tongue":8.3444601801,"year":90816.4971581012} +{"taxon":"fe30ff0f71a38a39cf1717ec2be3a2fc","(Intercept)":-861683502.712356925,"body-site::left palm":12.8611438894,"body-site::right palm":20.1786232328,"body-site::tongue":-1.1898355664,"year":83819.0848453717} +{"taxon":"868528ca947bc57b69ffdf83e6b73bae","(Intercept)":-961414485.8867735863,"body-site::left palm":16.4795912965,"body-site::right palm":8.1245010178,"body-site::tongue":-6.2934466966,"year":60330.7200633827} 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b/q2_composition/_da_barplot/tests/data/taxonomy-fake.tsv @@ -0,0 +1,8 @@ +Feature ID Taxon +1 d1;k1;p1 +2 d1;k1;p2 +3 d1;k2;p3 +4 d2;k1 +5 d1 +6 d2;k3;p4 +7 d2;k3;p4;c1 diff --git a/q2_composition/_da_barplot/tests/data/taxonomy.tsv b/q2_composition/_da_barplot/tests/data/taxonomy.tsv new file mode 100644 index 0000000..856183f --- /dev/null +++ b/q2_composition/_da_barplot/tests/data/taxonomy.tsv @@ -0,0 +1,771 @@ +Feature ID Taxon Confidence +4b5eeb300368260019c1fbc7a3c718fc k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__ 0.9958337221946401 +fe30ff0f71a38a39cf1717ec2be3a2fc k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__; s__ 0.9999428120610714 +d29fe3c70564fc0f69f2c03e0d1e5561 k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus; s__ 0.9999999999436398 +868528ca947bc57b69ffdf83e6b73bae k__Bacteria; p__Bacteroidetes; c__Bacteroidia; 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f__Prevotellaceae; g__; s__ 0.8226723721441197 +4fdf8dcd9451f5742982d716fa9f0536 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__Brachymonas; s__denitrificans 0.990341594080054 +4ea5683e2c2a183c11c45dc8fbd0c67c k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__ 0.9999999202641409 +469e4ff2129066178b74b112829fc03c k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__ 0.9999966339634149 +6edca9464612efff71d8f97299f01663 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 0.9888368635892377 +41fedaa9200e2933821f84ecdc0b0772 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Blautia; s__ 0.9998288585755445 +41735c13fb7f63db49b10fba5d959ce3 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__; s__ 0.9999922527995685 +54d098d009b89779530eaf43a1bb136a k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales; f__Pasteurellaceae; g__; s__ 0.9841307620937348 +76174505aef45f134d8068d5ad2c42aa k__Bacteria; p__Fusobacteria; c__Fusobacteriia; o__Fusobacteriales; f__Fusobacteriaceae; g__Cetobacterium; s__somerae 0.999989065299615 +b8afb7bb30b7a9170b7c6dcd40251d54 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.7910683742822175 +4c4606a3dbb4f5b8bb1ad1db6dfc5617 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__acnes 0.9814623426752663 +3ef461f213bfc675ddf0b1bfeef2dc52 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Alcaligenaceae; g__Sutterella; s__ 0.9348931942522047 +1f50ac250618ced095a2a5c34bae7651 k__Bacteria; p__Proteobacteria; c__Epsilonproteobacteria; o__Campylobacterales; f__Campylobacteraceae; g__Campylobacter; s__ 0.9998667199514364 +b3d4d129c955517b446df657236ba5a2 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__[Paraprevotellaceae] 0.7452402307199099 +fc15824cd9e9c29e1319d32843452b54 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfovibrionales; f__Desulfovibrionaceae; g__Desulfovibrio; s__ 0.9993291130018358 +f8f937eeee7762f446a0e87292f98eb6 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Parabacteroides; s__gordonii 0.9753745095429026 +b2866fdca13681232057e3e85a1978cf k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__ 0.9997867752403777 +052128d7d424728578efe7852b0afd0d k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.9763024906230429 +fc5b641a0b0408d99ddfb2a5ba64da59 k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__ 0.9999999961057711 +2514cdaab96a1a42cf15506f2ecf6439 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.8498350234496956 +e0472171de6fa02a1f58e392ad3d000e k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__ 0.9999999994890345 +e063d1c3c9daf7390e5475e48d9b01c5 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Lachnospira; s__ 0.9952238383416682 +958bc15b660bce0b894665d13f910f5b k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Anaerococcus; s__ 0.9999999462400823 +1b448e00c078f81e49a61933072345d2 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__; f__; g__; s__ 0.7665635644743813 +2e55763e77234a7bfc3a311067a0c7e1 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.9782290160244883 +162ed46308ef9dd1600fb0fe7c90b186 k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Lactobacillaceae; g__; s__ 0.9050911973312585 +9af77e369d2ba4b3bb6e0e808ed84d91 k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus; s__ 0.9999999987383887 +e77bac543df42865af751a32a2942fdb k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales 0.9999995997924442 +5ada68b9a081358e1a7d5f1d351e656a k__Bacteria; p__Fusobacteria; c__Fusobacteriia; o__Fusobacteriales; f__Leptotrichiaceae; g__Leptotrichia; s__ 0.999999999987125 +f8a71161ac98c5ceafcc75e57ace7230 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; g__Lardizabala; s__biternata 0.8749556659983647 +26b8b1509edf09c438db1634308c3c90 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__; s__ 0.7966856263546956 +3ae3e825c5e3862af6c17798e2b40a37 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Ruminococcus; s__ 0.8622175299699908 +26133b4163fdcd22d86f4e04e74154f1 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; 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f__[Mogibacteriaceae]; g__; s__ 0.9999722539035509 +d51cd90e95b57acb614698dc580759fb k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.953211007651201 +c5dfb8aa2b481cb89e2602fc20941587 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Porphyromonas; s__ 0.9809176799677424 +04c7e0ea3038f942f5a28778a74cd1c0 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales 0.999998162830321 +d12759fe8dda1d65fe9077cc1ca9cf28 k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales; f__Cryomorphaceae; g__; s__ 0.894645937459983 +44f993a57b632b8fde0c34ed075e1d66 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__; f__; g__; s__ 0.8224024521820277 +6401660183a33dded59f163fc63aab4d k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales 0.9771145132058217 +dc7d3610c77e7c118082f25002f26cd4 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides 0.7798962821568877 +1e9fc37a1112b198ed3d0543db7863c8 k__Bacteria; p__Fusobacteria; c__Fusobacteriia; o__Fusobacteriales; f__Leptotrichiaceae; g__Leptotrichia; s__ 0.9999999999967741 +685ea779ee012329ec2a171f1823f8a8 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__; s__ 0.8751644661590657 +1c0a00b159b2154357cc9bc7499c58b2 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Pseudonocardiaceae; g__Saccharomonospora; s__ 0.9392749640458771 +b0ca0d2568c23c26c6704017eae471e1 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales 0.9745960035993452 +1a8d25f7529d783a219ef689701dd4e2 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__[Barnesiellaceae]; g__; s__ 0.9927708072308242 +aa24dbd408e5d69c6b0d62846145a244 k__Bacteria; p__Firmicutes; c__Clostridia 0.7885985886563874 +cf8a25fe1a1b134a027842e7769a285b k__Bacteria; p__Bacteroidetes; c__[Saprospirae]; o__[Saprospirales]; f__Chitinophagaceae 0.9999958620579945 +b1e686a5c5f127a8b92de2863503a9e5 k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus; s__ 0.9999744495820918 +459244e45f29ce28991de0114a16f9fa k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Mogibacteriaceae]; g__Mogibacterium; s__ 0.9999746542265215 +491ef1635067f62c395bdffd58966092 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales 0.9998704003587595 +a03aa6a23dc8f296567452ec2242a5fd k__Bacteria; p__Actinobacteria; c__Coriobacteriia; o__Coriobacteriales; f__Coriobacteriaceae; g__; s__ 0.8998639028324782 +d32d15407d86a2044eead0d72cd3f9e7 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Veillonellaceae; g__; s__ 0.7847638533151173 +bb2704c9052362b112da42bf843e7d9b k__Bacteria; p__Bacteroidetes; c__[Saprospirae]; o__[Saprospirales]; f__Chitinophagaceae; g__Flavisolibacter; s__ 0.8870674213443654 +955280212814a2050dd2f640e10fc25d k__Bacteria; p__Fusobacteria; c__Fusobacteriia; o__Fusobacteriales; f__Leptotrichiaceae; g__Leptotrichia; s__ 0.9999999999451035 +684b032107a3a32f6664dea4ef723a42 k__Bacteria 0.9763699651056932 +d5ef913e6aee3067001dc610ac8af1d1 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__; g__; s__ 0.997736403622595 +e2cbf79a06f1221cf49d1bef8e5db9cd k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Peptostreptococcaceae; g__; s__ 0.9999998454990027 +3d6555a4886c6e4a89104136dd5ca39e k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Porphyromonas; s__ 0.9999999499447808 +d1c7ee5172f16dda522e46aaa4e5fa79 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__; s__ 0.8838505602666903 +74106ca246bcf2da5c4f95b82aa6867a k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodobacterales; f__Rhodobacteraceae; g__Paracoccus; s__marcusii 0.8969363728973645 +e80d9134b601511a2702b54268b57249 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__ 0.846467398652712 +3111520c8424a2a5bdd46558ae7650e8 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 0.986596475206643 +867e71db0537674539934bf97db51bc0 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 0.9671375895080958 +8c255f9dc0be58d1389877ec645f1a17 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Rhizobiaceae; g__; s__ 0.9374955192827125 +d30b3fb9c1dc7d9f0d4bd6ce8e975238 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__; g__; s__ 0.9650161287821856 +b1413b635612c7db2c140bc671789ec7 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae 0.9974656242062745 +12ed71ced0f4e45c0aa5b37144e6f84b k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Mogibacteriaceae]; g__Mogibacterium; s__ 0.9999925421901555 +3597a2689efaf5525ce460494a8ac383 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.9946055495174548 +3d6f762d8cda1915ad93d014e391c118 k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Leuconostocaceae; g__; s__ 0.9999999981794474 +7595e123b71bdae8a8c1c28b7405a5c0 k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Lactococcus; s__ 0.9807722690241437 +87a04eba5a3dc45f9e899d8ab4c050b4 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales 0.9996432667431419 +cbc2f795edfaebaf35d10b85062b426d k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales; f__Cryomorphaceae; g__; s__ 0.9881925141385922 +4738a05820f1a7840410c66476953498 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Porphyromonas; s__ 0.9713578612917114 +d9095748835ade1b8914c5f57b6acbcf k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Plesiomonas; s__shigelloides 0.9645705724989544 +1ca133f4d30ab344f11e6624e841d9cd k__Bacteria; p__Spirochaetes; c__Spirochaetes; o__Spirochaetales; f__Spirochaetaceae; g__Treponema; s__ 0.950703733856568 +6f384c926424d43c215fbe9337d55324 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__; f__; g__; s__ 0.8813456185136317 +f4eefbd4edf2a372131825289fffcca6 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__ 0.9995469607506324 +9f4cdae8a020a8d9c4f54e5abf5a5769 k__Bacteria 0.9999999613446524 +752621a2dcf600f86357e9c2fa1fc985 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Porphyromonas; s__ 0.9999999937560489 +6ffdeb862aed8aedda8a8624fa960c57 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__; s__ 0.9999443167941194 +faf2bd479f04891ef2afba2f407749ac k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 0.9743558729721384 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f__Clostridiaceae; g__; s__ 0.7428987191124414 +6a9b2745a31a3e5ae16682a323c28a4d k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria 0.9953764952290288 +7fa8f515ee1ac5cb8b529b13e6a89790 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales; f__Pasteurellaceae; g__Aggregatibacter; s__segnis 0.949381274176957 +c81e310dae79b8767597762a093082c8 k__Bacteria; p__Proteobacteria; c__Epsilonproteobacteria; o__Campylobacterales; f__Campylobacteraceae; g__Campylobacter; s__ 0.9976261105781868 +51588a76b68ff3041e8b272256df5ae2 k__Bacteria; p__Synergistetes; c__Synergistia; o__Synergistales; f__Dethiosulfovibrionaceae; g__TG5; s__ 0.9070807368354143 +a3dc97e11838f1bf157aa875f2f6367d k__Bacteria; p__Bacteroidetes 0.9999999055295461 +f351326f9505ffc18da207391818c48e k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodobacterales; f__Rhodobacteraceae; g__; s__ 0.9821277811324446 +53dd9f9a89854c8ebdcfb105b7a26df1 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Nocardioidaceae; g__; s__ 0.9991536366666571 +fbf110ef5de76f86121c8504a0cb786e k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 0.9465733411849421 +f66effc279917d65747b7c3ef8d62432 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__ 0.8328144562379329 +5c541619c0a084c6609e071895d9de55 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.9938955608311 +9b959f65abdb6cb9adc1d6160a5384ec k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__Allobaculum; s__ 0.9999999932852575 +a826883ed572461c97a23561f7ecea3c k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales; f__Flavobacteriaceae 0.972801149277789 +480b52afa972e6deb75357ec39db1998 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__MKC10; f__; g__; s__ 0.9999982632895144 +c961cc0ecd0ac693e2fb7dcf7794c3e5 k__Bacteria; p__Bacteroidetes; c__Flavobacteriia; o__Flavobacteriales; f__Flavobacteriaceae; g__Capnocytophaga; s__ochracea 0.9119933159074036 +ff8c7f94f941a0c647120d4e142db316 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Veillonellaceae; g__Dialister; s__ 0.9926398192142779 +e6df6369108817c93a749fa640528e92 k__Bacteria; p__Bacteroidetes; c__Cytophagia; o__Cytophagales; f__Flammeovirgaceae; g__; s__ 0.790311130955446 +e54bcf1c8ec24811e7c355b8d82fa59e k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Nocardioidaceae; g__; s__ 0.9999999890900001 +cee164362eb3296a3d29e33f7b479d2e k__Bacteria; p__Cyanobacteria; c__; o__; f__; g__; s__ 0.8789686234635555 +71e9ece7818452114b1e87f8145aefd5 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae 0.8132539537195868 +ae4c61e598c093caa5b66b6919f02ba3 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Hyphomicrobiaceae; g__; s__ 0.9418486227376394 +a54095a893fd5abc045d162bbe20644a k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae 0.908486538016183 +3253177a44672689e4e154e842d63e35 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales 0.9971138922337394 +45c36b8b2965484407b8b213419d4c6c k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Anaerococcus; s__ 0.999999693292712 +e9f0399c43aff643ceb1480929cf89b2 k__Bacteria; p__Spirochaetes; c__Spirochaetes; o__Spirochaetales; f__Spirochaetaceae; g__Treponema; s__socranskii 0.9999999999657732 +d985172bebaa0bbe61ff5f682d372c6e k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 0.9932764067703407 +02878fe3ccc81d4c884ca5574178d6a0 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.711487333195246 +a841dd7e2f38b26bb7bb37179b4141d5 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales 0.9979250398867832 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+216d5bb567182b6210e2c3dbc455f2b6 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__[Odoribacteraceae]; g__Odoribacter; s__ 0.9992778832225604 +a9541756b547061c02922f1a3a913fce k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__ 0.9185187935457652 +059408ca99f1001f64e6df1e06fb951d k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__ 0.739486211795697 +111311cc108c483f3782c9214681ed19 k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae 0.9824899905076373 +427e48835f176c1a367a14b39b882c58 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Porphyromonas; s__ 0.8118007388610889 +10ae3ca534ce9bb9f80822b4b4a6375c k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Rhizobiaceae; g__; s__ 0.9704669332421135 +8cfda573467e6a959664801713cadba1 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__ 0.9787326755629034 +73bca1b91fb8a80ee698f1833c073664 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__ 0.9335337718148026 +fc8f87209db793f740eea731e64f0b2a k__Bacteria 0.999997387393627 +9f6a3b261bc6acafa3d4a6d2de87f924 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Xanthomonadales; f__Xanthomonadaceae; g__Stenotrophomonas; s__maltophilia 0.8656053209210345 +b387961d274808e3ffed8c1594f4cd1c k__Bacteria; p__Actinobacteria; c__Acidimicrobiia; o__Acidimicrobiales; f__; g__; s__ 0.9999977144163921 +e1b32002ee69c4e3210a2a257511f96a k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Porphyromonas; s__ 0.9958404526334174 +6e342714744bf1b213ac0767d6c3998d k__Bacteria; p__[Thermi]; c__Deinococci; o__Deinococcales; f__Trueperaceae; g__B-42; s__ 0.7896352824675161 +14374c3f2fe75bb158b439ebe4a4ee87 k__Bacteria; p__Chloroflexi; c__Anaerolineae; o__Caldilineales; f__Caldilineaceae; g__; s__ 0.9999517458425682 +30d793622ebd90e7687dd3827701d46e k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 0.8752657828256205 +fe72a66c85df0ab333e3a37d0332df67 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Christensenellaceae; g__; s__ 0.8097925801642317 +bc15061b61cf6b5002c58284591f97d4 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Mogibacteriaceae]; g__; s__ 0.9999809866209918 +dbae1b46b67ad6769ea63d33ed3d44bf k__Bacteria; p__Firmicutes; c__Bacilli; o__Turicibacterales; f__Turicibacteraceae; g__Turicibacter; s__ 0.9999995307574245 +99acae6a2b24652d92a1ee4cbf8faca5 k__Bacteria 0.964368629661323 +d0dee8a51da30ed74bcadcd7d8e43537 k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Chlorophyta; f__; g__; s__ 0.9999999748914664 +8bcec52021ee6467bf008848d55b7a9f k__Bacteria; p__Verrucomicrobia; c__; o__; f__; g__; s__ 0.8466530175607863 +32a4d183139d99ace97a18b276d7c169 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales 0.8383514846450921 +524f22cecc9957e9bf629b5fb0047adc k__Bacteria; p__Bacteroidetes; c__Cytophagia; o__Cytophagales 0.998835395149775 +2fe6a7331192dc6bf073d906fba93929 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__ 0.9960386373852823 +be5ed9c02284fa6aa31037f0e2d93470 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria 0.9603087777874567 +8f146ce7c43f38ad3673dabe93c7c5bb k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__; g__; s__ 0.7037117244150338 +8dc69d65ac9e71a130bc6dbeb71d2f03 k__Bacteria 0.9697024932246691 +d30a7f0a26bd40402be57831cfa4da69 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria 0.8756456579124897 +26583b57be9de00bee14d30f2dc986d8 k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Chlorophyta; f__Trebouxiophyceae; g__; s__ 0.999999999118458 +254482075b19ff911db5e5cb26817498 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Aeromonadales; f__Aeromonadaceae; g__Tolumonas; s__ 0.7464095282022631 +21b849f15da11a7cc5122773552e0fef k__Bacteria; p__Chloroflexi 0.9857492495710293 +f59aa47df669ef50955ce1a0512d3abf k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__; g__; s__ 0.7555192450631512 +c89812744d8755bef87bedf499bd19cf k__Bacteria 0.9750146282643379 +f8fee8796e3188a996dfeca9e93f47e1 k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__Bulleidia; s__ 0.9980916227677465 +a3a69f621716f9345def32e2b5e7b011 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.9625163910766555 +5af6e343611d715985e35e7a3e5671cb k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Mogibacteriaceae]; g__; s__ 0.9311414150252683 +317c0beca40f29f3aff863b8f028fd48 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Gallicola; s__ 0.9997064291905559 +85943cff5ec22653bc51c22adeabe685 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; g__Acanthamoeba; s__culbertsoni 0.9970085820748956 +2c47de0940a8213b1ba751a7cd0b649b k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Rikenellaceae; g__AF12; s__ 0.9999999996227871 +14b20f972cfa94f77bc33eccc5ffca4c k__Bacteria; p__Verrucomicrobia; c__[Spartobacteria]; o__[Chthoniobacterales]; f__[Chthoniobacteraceae]; g__DA101; s__ 0.9999375839646749 +9cd758ad7582755a7f52f2b003787795 k__Bacteria; p__Proteobacteria; c__Epsilonproteobacteria; o__Campylobacterales; f__Helicobacteraceae 0.7884595852143892 +5d4a0085030ee808369a8f29be41e0d2 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales 0.7622592052499118 +c88977d348c943b60eea8f1571e9a7ee k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__durum 0.9365996565974561 +81e706ae981fcbfceea2ac547fdd7f26 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales 0.7007779955696168 +35bfc371d940cffdc527b7b4dc954456 k__Bacteria 0.8983347357171165 +4a146c717d33b2f2719e648bd7d22059 k__Bacteria; p__Planctomycetes; c__Planctomycetia; o__Planctomycetales; f__Planctomycetaceae; g__Planctomyces; s__ 0.9999999943921125 +541947958ad35c1591eb3ef433141196 k__Bacteria; p__Bacteroidetes; c__[Rhodothermi]; o__[Rhodothermales]; f__Rhodothermaceae; g__Rubricoccus; s__ 0.8368847606448594 +a95851baf426c85eae4419617db902a7 k__Bacteria 0.8839793133874827 +34f493c9b3b75210406fecac2dba0f22 k__Bacteria 0.99999999892876 +514a4ebb290842347e3f7ac7cbba276e k__Bacteria 0.977892724728328 +cfce45c3a7af608093fd99677d635891 k__Bacteria; p__Verrucomicrobia; c__[Spartobacteria]; o__[Chthoniobacterales]; f__[Chthoniobacteraceae]; g__Ellin506; s__ 0.826327166127106 +ef571c059fe495366b01e977f7494fbc k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Myxococcales; f__; g__; s__ 0.9982049095845408 +c73d4cf2ab0b699fb47d44488b82fd40 k__Bacteria; p__Verrucomicrobia; c__[Pedosphaerae]; o__[Pedosphaerales]; f__; g__; s__ 0.9997262972383966 +f79e815e1e628908e4ab605022b0ac09 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Mogibacteriaceae]; g__; s__ 0.9959606220122001 +23b560e97aacfd0422ed3f8a1104e7d7 k__Bacteria; p__Spirochaetes; c__Spirochaetes; o__Spirochaetales; f__Spirochaetaceae; g__Treponema; s__ 0.985995667905748 +eed50a4877de2fd21b146b4f0c7327ac k__Bacteria; p__Chloroflexi; c__Gitt-GS-136; o__; f__; g__; s__ 0.7923905965393132 +6d7d9658988c6e2b5e45ea087f1b9155 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Mogibacteriaceae]; g__Mogibacterium; s__ 0.9999530128058945 +502b6544978890cda2ece2d14bfdba01 k__Bacteria 0.9999992713823516 +ca08eabd09756731f095632656d45b01 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; g__; s__ 0.9983619317607827 +694caec8dad781d338acf4a5b69c3058 k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__Allobaculum; s__ 0.9933864641518518 +14e1a93cf2379225b1fd6ed0f186bacb k__Bacteria; p__FBP; c__; o__; f__; g__; s__ 0.9996710419708875 +6488fe0aaa024ba9c06647578b5a6caf k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodospirillales; f__Acetobacteraceae; g__Roseococcus; s__ 0.9995620152418827 +5ce3a51e54f30fa53b1e56dc64d11340 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales 0.9951843239239426 +4d987a66ee0e67b68c5c4428097eb22e k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Thiotrichales; f__Thiotrichaceae; g__CF-26; s__ 0.7994705971955715 +c3fd5b1d03591477953d49f0f19600c4 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfovibrionales; f__Desulfomicrobiaceae; g__; s__ 0.9999999993020481 +08bd73939f7bfd85daf2eaee7e9c9bf8 Unassigned 0.8664133093465773 +93a769a6b67e5f358eb9ad0e03c53ec3 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae] 0.9989722925004496 +654f282fc504b4dc9af5b8e66a4d1a87 k__Bacteria; p__GN02; c__BD1-5; o__; f__; g__; s__ 0.8937638443300449 +895453b352ae060e0ec5f7721547a3d1 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 0.7756571434765006 +b29143b255f4b97da62310d85fe9b7f3 k__Bacteria; p__Firmicutes; c__Clostridia 0.7084783782168641 +95dff3e66b8bdf4d8e509ceae4373c69 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Lachnospira; s__ 0.9997983395343405 +da3328e15aae60ea55a8765511d0327e k__Bacteria; p__Verrucomicrobia; c__[Pedosphaerae]; o__[Pedosphaerales]; f__; g__; s__ 0.999999885192515 +ebcbd71a778e6a1a776d2d50d0801fed k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__ 0.9975013045776004 +c80037fe31359840bb73250f330b60e3 k__Bacteria 0.9727262121442337 +bd759efe26a5b4b869d3fa5e4693080d k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__ 0.9995981370005347 +723858f72b4469efb79c323f75bc181f k__Bacteria; p__Planctomycetes; c__Planctomycetia; o__Planctomycetales; f__Planctomycetaceae; g__Planctomyces; s__ 0.9999842079365734 +8021f872c32700d46738f3591cb4c58a k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 0.950298422800317 +47c7eb4df73a5d553cd2f7a360ff5872 k__Bacteria 0.9625306758187444 +ad492bcae03f566b36a19e31f04d659a k__Bacteria 0.9592420622809142 +eb8ef4756ed538fe480d979e740a04d8 k__Bacteria 0.9992518268672295 +5db2cf37007f874e25eb2c901917e15a k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__ 0.9998650088122101 +fa3729663b98de0c0af7913e9f30c19e k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodospirillales; f__; g__; s__ 0.7260248247151302 +504572e3afd673db749ee5e8e3e57b97 k__Bacteria; p__Cyanobacteria 0.996420061481882 +a6b6f29a1196cacfc392e3d71f55e2a2 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Bdellovibrionales; f__Bacteriovoracaceae; g__Bacteriovorax; s__ 0.9536660457678927 +0e5df3d01cc073e3c9674c2534169f03 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Acidaminobacteraceae]; g__Acidaminobacter; s__ 0.749393658744113 +06845c67bc4203081a981200f33e87eb k__Bacteria; p__Proteobacteria 0.9956180804506998 +98d250a339a635f20e26397dafc6ced3 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__ 0.999193575156621 +1830c14ead81ad012f1db0e12f8ab6a4 k__Bacteria; p__TM7; c__TM7-3; o__Blgi18; f__; g__; s__ 0.9226796920359376 diff --git a/q2_composition/_da_barplot/tests/featureRecord.test.ts b/q2_composition/_da_barplot/tests/featureRecord.test.ts new file mode 100644 index 0000000..4f7b01e --- /dev/null +++ b/q2_composition/_da_barplot/tests/featureRecord.test.ts @@ -0,0 +1,93 @@ +import { describe, test, assert } from "vitest"; +import { FeatureRecord, FeatureRecords } from "../src/util/features"; + +describe("FeatureRecord class", () => { + const feature = new FeatureRecord("abc123"); + + feature.addVariable( + feature.createVariable("body-site", "lfc", 2.2, "tongue", "gut"), + ); + feature.addVariable( + feature.createVariable("body-site", "lfc", -0.3, "left palm", "gut"), + ); + feature.addVariable( + feature.createVariable("body-site", "p", 0.05, "left palm", "gut"), + ); + + test("addVariable()", () => { + assert.equal(feature.variables.size, 2); + }); + + test("getVariable()", () => { + let obs = feature.getVariable("body-site", "tongue"); + let exp = { + name: "body-site", + lfc: 2.2, + level: "tongue", + reference: "gut", + }; + assert.deepEqual(obs, exp); + + obs = feature.getVariable("body-site", "left palm"); + exp = { + name: "body-site", + lfc: -0.3, + p: 0.05, + level: "left palm", + reference: "gut", + }; + assert.deepEqual(obs, exp); + }); + + test("getVariableSlice()", () => { + let obs = feature.getVariableSlice("body-site", "lfc", "tongue"); + let exp = 2.2; + assert.equal(obs, exp); + + obs = feature.getVariableSlice("body-site", "p", "left palm"); + exp = 0.05; + assert.equal(obs, exp); + }); +}); + +describe("FeatureRecords class", () => { + const features = new FeatureRecords(); + + const feature1 = new FeatureRecord("abc123"); + feature1.addVariable( + feature1.createVariable("body-site", "lfc", 2.2, "tongue", "gut"), + ); + feature1.addVariable( + feature1.createVariable("body-site", "lfc", -0.3, "left palm", "gut"), + ); + + features.addFeature(feature1); + + test("addFeature()", () => { + assert.equal(features.records.length, 1); + }); + + const feature2 = new FeatureRecord("abc123"); + feature2.addVariable( + feature2.createVariable("body-site", "p", 0.05, "left palm", "gut"), + ); + features.addFeature(feature2); + + test("addFeature() matching feature", () => { + assert.equal(features.records.length, 1); + + assert.equal(features.records[0].variables.size, 2); + }); + + test("addFeature() merges features", () => { + assert.equal(features.records.length, 1); + + const feature = features.getFeature("abc123"); + + const lfc = feature!.getVariableSlice("body-site", "lfc", "left palm"); + assert.equal(lfc, -0.3); + + const p = feature!.getVariableSlice("body-site", "p", "left palm"); + assert.equal(p, 0.05); + }); +}); diff --git a/q2_composition/_da_barplot/tests/parse.test.ts b/q2_composition/_da_barplot/tests/parse.test.ts new file mode 100644 index 0000000..b1065a7 --- /dev/null +++ b/q2_composition/_da_barplot/tests/parse.test.ts @@ -0,0 +1,168 @@ +import { vi, describe, test, assert } from "vitest"; +import { readFileSync } from "fs"; +import { FeatureRecords } from "../src/util/features"; +import { + getColumnField, + parseJSONLFeatureRecord, + parseSlice, + parseAllSlices, +} from "../src/util/parse"; + +// mock d3.text +async function mockedText(slice: string): Promise { + return readFileSync(slice, "utf-8"); +} +vi.mock("d3-fetch", () => { + return { text: vi.fn(mockedText) }; +}); + +describe("getColumnField()", () => { + const lfcText = readFileSync("tests/data/output-format/lfc.jsonl", "utf-8"); + const header = JSON.parse(lfcText.split("\n")[0]); + + test("column name is present", () => { + const column = "body-site::left palm"; + const exp = { + name: "body-site::left palm", + type: null, + missing: false, + title: "", + description: "", + extra: { + variable: "body-site", + level: "left palm", + reference: "gut", + }, + }; + + assert.deepEqual(getColumnField(column, header), exp); + }); + + test("column name not present", () => { + const column = "waldo"; + + assert.throws( + () => getColumnField(column, header), + "Column waldo not found in JSONL header.", + ); + }); +}); + +describe("parseJSONLFeatureRecord()", () => { + const lfcText = readFileSync("tests/data/output-format/lfc.jsonl", "utf-8"); + const jsonRecords = lfcText + .split("\n") + .filter((line) => line.trim() !== "") + .map((line) => JSON.parse(line)); + + const header = jsonRecords[0]; + const jsonRecord = jsonRecords[1]; + const sliceName = "lfc"; + + const obs = parseJSONLFeatureRecord(jsonRecord, header, sliceName); + + test("parses feature id", () => { + assert.equal(obs.featureId, "4b5eeb300368260019c1fbc7a3c718fc"); + }); + + test("parses correct number of variables", () => { + assert.equal(obs.variables.size, 5); + }); + + test("parses categorical columns", () => { + const variables = Array.from(obs.variables.values()); + const bodySiteVariables = variables.filter( + (v) => v.name == "body-site", + ); + assert.equal(bodySiteVariables.length, 3); + + const levels = bodySiteVariables.map((v) => v.level); + assert.sameMembers(levels, ["right palm", "left palm", "tongue"]); + + const references = bodySiteVariables.map((v) => v.reference); + assert.sameMembers(references, ["gut", "gut", "gut"]); + }); + + test("parses numerical columns", () => { + const variables = Array.from(obs.variables.values()); + const nonCategoricalVariables = variables.filter( + (v) => !Object.hasOwn(v, "reference"), + ); + assert.equal(nonCategoricalVariables.length, 2); + + const yearVariable = nonCategoricalVariables.find( + (v) => v.name == "year", + ); + assert.deepEqual(yearVariable, { + name: "year", + lfc: 189.6871124062, + }); + }); +}); + +describe("parseSlice()", async () => { + const sliceFilepath = "tests/data/output-format/lfc.jsonl"; + const featureRecords = new FeatureRecords(); + await parseSlice(sliceFilepath, featureRecords); + + test("correct number of features", () => { + assert.equal(featureRecords.records.length, 8); + }); + + test("slice parsed correctly", () => { + const feature = featureRecords.getFeature( + "fe30ff0f71a38a39cf1717ec2be3a2fc", + ); + + assert.equal( + feature!.getVariableSlice("body-site", "lfc", "left palm"), + 113.4173262332, + ); + + assert.equal(feature!.getVariableSlice("year", "lfc"), 181.01108921); + + const variable = feature!.getVariable("body-site", "right palm"); + assert.isOk(variable!.lfc); + assert.isNotOk(variable!.q); + assert.isNotOk(variable!.p); + assert.isNotOk(variable!.se); + }); +}); + +describe("parseAllSlices()", async () => { + const sliceDirPath = "tests/data/output-format"; + const featureRecords = new FeatureRecords(); + await parseAllSlices(sliceDirPath, featureRecords); + + test("correct number of features", () => { + assert.equal(featureRecords.records.length, 8); + }); + + test("all slices parsed", () => { + for (let featureRecord of featureRecords.records) { + for (let variable of featureRecord.variables.values()) { + for (let prop of ["lfc", "se", "p", "q"]) { + assert.property(variable, prop); + assert.isDefined(variable[prop]); + } + } + } + }); + + test("structure and contents of arbitrary feature", () => { + const id = "1d2e5f3444ca750c85302ceee2473331"; + const feature = featureRecords.getFeature(id); + + assert.equal( + feature!.getVariableSlice("body-site", "lfc", "left palm"), + 86.9453579935, + ); + + assert.equal(feature!.getVariableSlice("year", "se"), 0.0030650395); + + assert.property( + feature!.getVariable("body-site", "tongue"), + "reference", + ); + }); +}); diff --git a/q2_composition/_da_barplot/tests/taxonomy.test.ts b/q2_composition/_da_barplot/tests/taxonomy.test.ts new file mode 100644 index 0000000..7af4b73 --- /dev/null +++ b/q2_composition/_da_barplot/tests/taxonomy.test.ts @@ -0,0 +1,52 @@ +import { vi, describe, test, assert } from "vitest"; +import { readFileSync } from "fs"; +import { TaxonomyNode, parseTaxonomy } from "../src/util/taxonomy"; +import * as d3 from "d3"; + +// mock d3.tsv +async function mockedTsv(slice: string): Promise { + const textData = readFileSync(slice, "utf-8"); + let lines = textData.split("\n").filter((l) => l.trim() != ""); + + // drop header + lines = lines.slice(1); + + let data: object[] = []; + for (let line of lines) { + const values = line.split("\t"); + const record = { + "Feature ID": values[0], + Taxon: values[1], + }; + data.push(record); + } + + return data; +} +vi.mock("d3-fetch", () => { + return { tsv: vi.fn(mockedTsv) }; +}); + +describe("parseTaxonomy()", async () => { + let root: d3.HierarchyNode; + + test("parses successfully", async () => { + root = await parseTaxonomy("tests/data/taxonomy-fake.tsv"); + }); + + test("has correct number of nodes", () => { + assert.equal(root.descendants().length, 12); + }); + + test("root has correct children", () => { + const exp = ["d1", "d2"]; + assert.deepEqual( + root.children!.map((c) => c.data.name), + exp, + ); + }); + + test("back references exist", () => { + assert.equal(root.data.hierarchyNode, root); + }); +}); diff --git a/q2_composition/_da_barplot/tsconfig.app.json b/q2_composition/_da_barplot/tsconfig.app.json new file mode 100644 index 0000000..55a2f9b --- /dev/null +++ b/q2_composition/_da_barplot/tsconfig.app.json @@ -0,0 +1,20 @@ +{ + "extends": "@tsconfig/svelte/tsconfig.json", + "compilerOptions": { + "target": "ESNext", + "useDefineForClassFields": true, + "module": "ESNext", + "resolveJsonModule": true, + /** + * Typecheck JS in `.svelte` and `.js` files by default. + * Disable checkJs if you'd like to use dynamic types in JS. + * Note that setting allowJs false does not prevent the use + * of JS in `.svelte` files. + */ + "allowJs": true, + "checkJs": true, + "isolatedModules": true, + "moduleDetection": "force" + }, + "include": ["src/**/*.ts", "src/**/*.js", "src/**/*.svelte"] +} diff --git a/q2_composition/_da_barplot/tsconfig.json b/q2_composition/_da_barplot/tsconfig.json new file mode 100644 index 0000000..1ffef60 --- /dev/null +++ b/q2_composition/_da_barplot/tsconfig.json @@ -0,0 +1,7 @@ +{ + "files": [], + "references": [ + { "path": "./tsconfig.app.json" }, + { "path": "./tsconfig.node.json" } + ] +} diff --git a/q2_composition/_da_barplot/tsconfig.node.json b/q2_composition/_da_barplot/tsconfig.node.json new file mode 100644 index 0000000..db0becc --- /dev/null +++ b/q2_composition/_da_barplot/tsconfig.node.json @@ -0,0 +1,24 @@ +{ + "compilerOptions": { + "tsBuildInfoFile": "./node_modules/.tmp/tsconfig.node.tsbuildinfo", + "target": "ES2022", + "lib": ["ES2023"], + "module": "ESNext", + "skipLibCheck": true, + + /* Bundler mode */ + "moduleResolution": "bundler", + "allowImportingTsExtensions": true, + "isolatedModules": true, + "moduleDetection": "force", + "noEmit": true, + + /* Linting */ + "strict": true, + "noUnusedLocals": true, + "noUnusedParameters": true, + "noFallthroughCasesInSwitch": true, + "noUncheckedSideEffectImports": true + }, + "include": ["vite.config.ts"] +} diff --git a/q2_composition/_da_barplot/vite.config.ts b/q2_composition/_da_barplot/vite.config.ts new file mode 100644 index 0000000..bfeb276 --- /dev/null +++ b/q2_composition/_da_barplot/vite.config.ts @@ -0,0 +1,9 @@ +import { defineConfig } from "vite"; +import { svelte } from "@sveltejs/vite-plugin-svelte"; +import tailwindcss from "@tailwindcss/vite"; + +// https://vite.dev/config/ +export default defineConfig({ + plugins: [svelte(), tailwindcss()], + base: "", +}); diff --git a/q2_composition/_diff_abundance_plots.py b/q2_composition/_diff_abundance_plots.py deleted file mode 100644 index 29baa99..0000000 --- a/q2_composition/_diff_abundance_plots.py +++ /dev/null @@ -1,242 +0,0 @@ -# ---------------------------------------------------------------------------- -# Copyright (c) 2016-2026, QIIME 2 development team. -# -# Distributed under the terms of the Modified BSD License. -# -# The full license is in the file LICENSE, distributed with this software. -# ---------------------------------------------------------------------------- -import importlib.resources -from pathlib import Path -import urllib.parse -from collections import Counter - -import altair as alt -import pandas as pd -import numpy as np - -import qiime2 -from q2_composition import DataLoafPackageDirFmt -import q2templates - - -def _plot_differentials( - output_dir, - df, - title, - feature_id_label, - effect_size_label, - significance_label, - error_label, - feature_ids, - effect_size_threshold, - significance_threshold, - level_delimiter, - label_limit): - - if len(df) == 0: - raise ValueError("No features present in input.") - - # ensure that all columns are of the types required internally - df = df.astype({feature_id_label: pd.StringDtype(), - error_label: pd.Float64Dtype(), - significance_label: pd.Float64Dtype(), - effect_size_label: pd.Float64Dtype()}) - - if feature_ids is not None: - df = df.query(f'`{feature_id_label}` in @feature_ids') - - df = df[df[significance_label] <= significance_threshold] - df = df[np.abs(df[effect_size_label]) >= effect_size_threshold] - - if len(df) == 0: - raise ValueError("No features remaining after applying filters.") - - output_dir = Path(output_dir) - output_dir.mkdir(parents=True, exist_ok=True) - safe_title = urllib.parse.quote(title) - fig_fn = Path(f'{safe_title}-ancombc-barplot.html') - fig_fp = output_dir / fig_fn - - if level_delimiter is not None: - # For readability, only the most specific named taxonomy will be - # included in the y-axis label. The full taxonomy text will be in - # the tool-tip. Because it's possible that the most specific - # taxonomic name are not unique, this code simply prepends a number - # to names. Providing separate labels for ticks, which - # would avoid this, doesn't seem straight-forward in altair (e.g., - # see https://github.com/altair-viz/altair/issues/938). - y_labels = [] - seen = Counter() - for i, e in enumerate(df[feature_id_label]): - if level_delimiter in e: - fields = [field for field in e.split(level_delimiter) - if not field.endswith('__')] - else: - # this is necessary to handle a case where the delimiter - # isn't found and the e ends with '__' - fields = [e] - most_specific = fields[-1] - if most_specific in seen: - y_labels.append(f"{seen[most_specific]}: {most_specific} *") - else: - y_labels.append(most_specific) - seen[most_specific] += 1 - df['y_label'] = y_labels - df['feature'] = [id_.replace(level_delimiter, ' ') - for id_ in df[feature_id_label]] - else: - df['y_label'] = df['feature'] = df[feature_id_label] - - df['enriched'] = ["enriched" if x else "depleted" - for x in df[effect_size_label] > 0] - - df['error-upper'] = df[effect_size_label] + df[error_label] - df['error-lower'] = df[effect_size_label] - df[error_label] - - # Normally we would call bars.mark_rule to add standard error marks - # (opposed to alt.Chart.mark_bar, but I want to color the the standard - # error marks differently so they stand out against the bars themselves. - # As far as I can tell, I can only do this by creating two separate charts, - # so this shared y-axis will be used for both of those. - shared_y = alt.Y("y_label", - title="Feature ID", - sort=alt.EncodingSortField(field=effect_size_label, - op="min", order="descending")) - - bars = alt.Chart(df).mark_bar().encode( - x=alt.X('lfc', title="Log Fold Change (LFC)"), - y=shared_y, - tooltip=alt.Tooltip(["feature", effect_size_label, - significance_label, error_label, - "error-lower", "error-upper"]), - color=alt.Color('enriched', title="Relative to reference", - scale=alt.Scale( - domain=["enriched", "depleted"], - range=["#4c78a8", "#f58518"]), - sort="descending") - ) - - error = alt.Chart(df).mark_rule(color='black').encode( - x='error-lower', - x2='error-upper', - y=shared_y, - ) - - chart = (bars + error).properties(title=title) - chart = chart.configure_legend( - strokeColor='gray', - padding=10, - cornerRadius=10, - ) - - # Moves the y-axis title to the top-left, making it more apparent when - # there are a lot of features. - chart = chart.configure_axisY(titleAlign='left', - titleY=-10, titleAngle=0) - if label_limit is not None: - chart = chart.configure_axis(labelLimit=label_limit) - - chart.save(fig_fp) - return fig_fp - - -def da_barplot(output_dir: str, - data: DataLoafPackageDirFmt, - effect_size_label: str = 'lfc', - feature_id_label: str = 'id', - error_label: str = 'se', - significance_label: str = 'q_val', - significance_threshold: float = 1.0, - effect_size_threshold: float = 0.0, - feature_ids: qiime2.Metadata = None, - level_delimiter: str = None, - label_limit: int = None): - - # setup for the index.html page - ASSETS = importlib.resources.files('q2_composition') / 'assets' - index = Path(ASSETS, 'diff_abundance_plots', 'index.html') - - # collect the user-provided labels for validation - provided_slice_labels = set([effect_size_label, - significance_label, - error_label]) - - slice_data = {} - for e in data.data_slices.iter_views(pd.DataFrame): - slice_data[str(e[0]).replace('_slice.csv', '')] = e[1] - - observed_slice_labels = set(slice_data.keys()) - missing_slice_labels = provided_slice_labels - observed_slice_labels - if len(missing_slice_labels) > 0: - raise KeyError( - f"Provide label(s) ({' '.join(missing_slice_labels)}) " - "are not present in input. Available options are: " - f"{' '.join(observed_slice_labels)}.") - - # exclude the Intercept column from plots - column_labels = [e for e in slice_data[effect_size_label].columns - if e not in '(Intercept)'] - - if feature_id_label not in column_labels: - raise KeyError(f"Feature id header \"{feature_id_label}\" is not " - "present in input. Available options are: " - f"{' '.join(column_labels)}.") - - # create figure_data, which contains the cross-slice data for each - # column of the input dataloaf. some of this logic likely makes sense - # to move into a transformer which handles the arrangement of data - # into a multi-index dataframe. - # - # if the input dataloaf looks like: - # slice1: lfc - # feature-id skin gut - # f1 0.2 5.4 - # f2 1.2 0.1 - # slice2: q_value - # feature-id skin gut - # f1 0.9 0.01 - # f2 0.05 0.8 - # - # figure_data for a specific category will look like: - # feature-id lfc q_value - # f1 0.2 0.9 - # f2 1.2 0.05 - # or: - # feature-id lfc q_value - # f1 5.4 0.01 - # f2 0.1 0.8 - figure_data = [] - for column_label in column_labels: - if column_label == feature_id_label: - continue - df = pd.concat( - [slice_data[effect_size_label][feature_id_label], - slice_data[effect_size_label][column_label], - slice_data[error_label][column_label], - slice_data[significance_label][column_label]], - keys=[feature_id_label, effect_size_label, - error_label, significance_label], - axis=1) - - try: - figure_fp = _plot_differentials( - output_dir, df, - title=column_label, - effect_size_label=effect_size_label, - feature_id_label=feature_id_label, - error_label=error_label, - significance_label=significance_label, - significance_threshold=significance_threshold, - effect_size_threshold=effect_size_threshold, - feature_ids=feature_ids, - level_delimiter=level_delimiter, - label_limit=label_limit) - figure_fn = figure_fp.parts[-1] - figure_data.append((True, figure_fn, column_label, None)) - except ValueError as e: - figure_data.append((False, None, column_label, str(e))) - - context = { - 'figures': figure_data - } - q2templates.render(str(index), output_dir, context=context) diff --git a/q2_composition/plugin_setup.py b/q2_composition/plugin_setup.py index e374399..e81fc78 100644 --- a/q2_composition/plugin_setup.py +++ b/q2_composition/plugin_setup.py @@ -291,25 +291,24 @@ ) plugin.visualizers.register_function( - function=q2_composition.ancombc2_visualizer, + function=q2_composition.da_barplot, inputs={ 'data': FeatureData[DifferentialAbundance | ANCOMBC2Output], 'taxonomy': FeatureData[Taxonomy], }, parameters={}, input_descriptions={ - 'data': 'The ANCOMBC2 output to visualize.', + 'data': 'The ANCOMBC or ANCOMBC2 output to visualize.', 'taxonomy': ( - 'The taxonomy associated with the features present in the ' - 'ANCOMBC2 data.' + 'The taxonomy associated with the features present in the data.' ) }, - name='Visualize ANCOMBC2 output.', + name='Visualize ANCOMBC/ANCOMBC2 output.', description=( - 'Displays ANCOMBC2 Log-Fold Change values in a barplot and allows ' - 'filtering based on p-value and standard error. If a taxonomy is ' - 'provided, features can be filtered by taxonomy using an interactive ' - 'tree.' + 'Displays ANCOMBC/ANCOMBC2 Log-Fold Change values in a barplot and ' + 'allows filtering based on p-value and standard error. If a taxonomy ' + 'is provided, features can be filtered by taxonomy using an ' + 'interactive tree.' ), ) @@ -327,48 +326,4 @@ ' (se), P values, Q values, and W scores.' ), ) - -plugin.visualizers.register_function( - function=q2_composition.da_barplot, - inputs={'data': FeatureData[DifferentialAbundance]}, - parameters={'effect_size_label': Str, - 'feature_id_label': Str, - 'error_label': Str, - 'significance_label': Str, - 'significance_threshold': Float % Range(0.0, 1.0, - inclusive_start=True, - inclusive_end=True), - 'effect_size_threshold': Float % Range(0.0, np.inf, - inclusive_start=True), - 'feature_ids': Metadata, - 'level_delimiter': Str, - 'label_limit': Int}, - input_descriptions={'data': 'The ANCOM-BC output to be plotted.'}, - parameter_descriptions={ - 'effect_size_label': "Label for effect sizes in `data`.", - 'feature_id_label': "Label for feature ids in `data`.", - 'error_label': "Label for effect size errors in `data`.", - 'significance_label': ("Label for statistical significance " - "level in `data`."), - 'significance_threshold': ("Exclude features with statistical " - "significance level greater (i.e., less " - "significant) than this threshold."), - 'effect_size_threshold': ("Exclude features with an absolute value " - "of effect size less than this threshold."), - 'feature_ids': ("Exclude features if their ids are not included in " - "this index."), - 'level_delimiter': ("If feature ids encode hierarchical information, " - "split the levels when generating feature labels " - "in the visualization using this delimiter."), - 'label_limit': ("Set the maximum length that will be viewable for " - "axis labels. You can set this parameter if your " - "axis labels are being cut off.")}, - name='Differential abundance bar plots', - description=('Generate bar plot views of ANCOM-BC output. One plot will ' - 'be present per column in the ANCOM-BC output. The ' - '`significance_threshold`, `effect_size_threshold` ' - 'and `feature_ids` filter results are intersected, ' - 'such that only features that remain after all three ' - 'filters have been applied will be present in the output.'), -) importlib.import_module('q2_composition._transformer') diff --git a/q2_composition/tests/test_ancombc2.py b/q2_composition/tests/test_ancombc2.py index 9ec8ebf..c45159d 100644 --- a/q2_composition/tests/test_ancombc2.py +++ b/q2_composition/tests/test_ancombc2.py @@ -24,7 +24,7 @@ r_base, ancombc2, _process_formula, _convert_metadata, _split_into_slices, _rename_variables_post, _is_categorical, _parse_variable_and_level, _deduce_reference_levels, _process_categorical_variables, - _process_structural_zeros, ancombc2_visualizer + _process_structural_zeros, da_barplot ) from q2_composition._format import ANCOMBC2SliceMapping @@ -185,17 +185,17 @@ def test_spaces_in_metadata_column(self): # three levels, so one reference and other two in the output self.assertEqual(len(variable_with_spaces_columns), 2) - def test_ancombc2_visualizer(self): + def test_da_barplot(self): ''' Tests that the visualizer runs successfully, which is essentially a test of whether or not the visualizer got built into the - q2_composition/_ancombc2_visualizer/dist/ folder successfully. + q2_composition/_da_barplot/dist/ folder successfully. ''' with tempfile.TemporaryDirectory() as tempdir: - ancombc2_visualizer(tempdir, self.abc2_output) + da_barplot(tempdir, self.abc2_output) assert os.path.exists(os.path.join(tempdir, 'index.html')) - def test_ancombc2_visualizer_non_overlapping_taxonomy(self): + def test_da_barplot_non_overlapping_taxonomy(self): ''' Tests that an error is raised when attempting to visualize ancombc2 data with a taxonomy that contains none of the features present in the @@ -211,7 +211,7 @@ def test_ancombc2_visualizer_non_overlapping_taxonomy(self): with self.assertRaisesRegex( ValueError, 'No features remained in your taxonomy' ): - ancombc2_visualizer(tempdir, self.abc2_output, taxonomy_df) + da_barplot(tempdir, self.abc2_output, taxonomy_df) class TestFormulaProcessing(TestANCOMBC2Base): diff --git a/q2_composition/tests/test_diff_abundance_plot.py b/q2_composition/tests/test_diff_abundance_plot.py deleted file mode 100644 index 6491033..0000000 --- a/q2_composition/tests/test_diff_abundance_plot.py +++ /dev/null @@ -1,564 +0,0 @@ -# ---------------------------------------------------------------------------- -# Copyright (c) 2016-2026, QIIME 2 development team. -# -# Distributed under the terms of the Modified BSD License. -# -# The full license is in the file LICENSE, distributed with this software. -# ---------------------------------------------------------------------------- -import tempfile -from pathlib import Path -import urllib.parse - -from qiime2.plugin.testing import TestPluginBase -from qiime2 import Artifact - -from q2_composition import (da_barplot, DataLoafPackageDirFmt) - - -class TestBase(TestPluginBase): - package = 'q2_composition.tests' - - def setUp(self): - super().setUp() - self.dataloaf1 = Artifact.load(self.get_data_path('dataloaf.qza')) - self.dataloaf2 = \ - Artifact.load(self.get_data_path('dataloaf-hmp1-body-habitat.qza')) - - -class TestDABarplot(TestBase): - - def _get_output_filepath(self, dir, title): - safe_title = urllib.parse.quote(title) - return dir / f'{safe_title}-ancombc-barplot.html' - - def test_basic_dl1(self): - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf1.view(DataLoafPackageDirFmt), - feature_id_label='id') - self.assertTrue((output_dir / 'index.html').exists()) - - tongue_path = self._get_output_filepath( - output_dir, 'bodysitetongue') - self.assertTrue(tongue_path.exists()) - - right_palm_path = self._get_output_filepath( - output_dir, 'bodysiteright palm') - self.assertTrue(right_palm_path.exists()) - - left_palm_path = self._get_output_filepath( - output_dir, 'bodysiteleft palm') - self.assertTrue(left_palm_path.exists()) - - # checking that spaces are converted to %20 - left_palm_path = self._get_output_filepath( - output_dir, 'bodysiteleft palm') - fp = str(left_palm_path) - expected_fp_segment = "bodysiteleft%20palm-ancombc-barplot.html" - self.assertIn(expected_fp_segment, fp) - - # file shouldn't exist for reference column - gut_path = self._get_output_filepath( - output_dir, 'bodysitegut') - self.assertFalse(gut_path.exists()) - - # spot check for a feature id - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(tongue_path).read()) - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(right_palm_path).read()) - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(left_palm_path).read()) - - def test_basic_dl2(self): - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf2.view(DataLoafPackageDirFmt)) - self.assertTrue((output_dir / 'index.html').exists()) - - feces_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:feces') - self.assertTrue(feces_path.exists()) - - oral_cavity_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:oral cavity') - self.assertTrue(oral_cavity_path.exists()) - - saliva_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:saliva') - self.assertTrue(saliva_path.exists()) - - vagina_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:vagina') - self.assertTrue(vagina_path.exists()) - - # file shouldn't exist for reference column - skin_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:skin') - self.assertFalse(skin_path.exists()) - - # spot check for a feature id - self.assertTrue( - 'g__Staphylococcus' in - open(feces_path).read()) - self.assertTrue( - 'g__Staphylococcus' in - open(oral_cavity_path).read()) - self.assertTrue( - 'g__Staphylococcus' in - open(saliva_path).read()) - self.assertTrue( - 'g__Staphylococcus' in - open(vagina_path).read()) - - def test_label_limit(self): - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf2.view(DataLoafPackageDirFmt), - label_limit=4242) - feces_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:feces') - self.assertTrue('{"labelLimit": 4242}' in open(feces_path).read()) - - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf2.view(DataLoafPackageDirFmt), - label_limit=None) - feces_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:feces') - self.assertFalse('labelLimit' in open(feces_path).read()) - - def test_filter_on_significance(self): - # confirm feature presence when not filtering - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf1.view(DataLoafPackageDirFmt), - feature_id_label='id', - significance_threshold=1.0) - tongue_path = self._get_output_filepath( - output_dir, 'bodysitetongue') - self.assertTrue(tongue_path.exists()) - - right_palm_path = self._get_output_filepath( - output_dir, 'bodysiteright palm') - self.assertTrue(right_palm_path.exists()) - - left_palm_path = self._get_output_filepath( - output_dir, 'bodysiteleft palm') - self.assertTrue(left_palm_path.exists()) - - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(tongue_path).read()) - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(right_palm_path).read()) - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(left_palm_path).read()) - - # confirm feature absence when filtering - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf1.view(DataLoafPackageDirFmt), - feature_id_label='id', - significance_threshold=1e-3) - - tongue_path = self._get_output_filepath( - output_dir, 'bodysitetongue') - self.assertTrue(tongue_path.exists()) - - right_palm_path = self._get_output_filepath( - output_dir, 'bodysiteright palm') - self.assertTrue(right_palm_path.exists()) - - left_palm_path = self._get_output_filepath( - output_dir, 'bodysiteleft palm') - self.assertTrue(left_palm_path.exists()) - - # this feature is significant at this - # threshold only in tongue and left palm - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(tongue_path).read()) - self.assertFalse( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(right_palm_path).read()) - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(left_palm_path).read()) - - def test_filter_on_effect_size(self): - # confirm feature presence when not filtering - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf1.view(DataLoafPackageDirFmt), - feature_id_label='id', - effect_size_threshold=0) - - tongue_path = self._get_output_filepath( - output_dir, 'bodysitetongue') - self.assertTrue(tongue_path.exists()) - - right_palm_path = self._get_output_filepath( - output_dir, 'bodysiteright palm') - self.assertTrue(right_palm_path.exists()) - - left_palm_path = self._get_output_filepath( - output_dir, 'bodysiteleft palm') - self.assertTrue(left_palm_path.exists()) - - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(tongue_path).read()) - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(right_palm_path).read()) - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(left_palm_path).read()) - - # confirm feature absence when filtering - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf1.view(DataLoafPackageDirFmt), - feature_id_label='id', - effect_size_threshold=3.5) - - tongue_path = self._get_output_filepath( - output_dir, 'bodysitetongue') - self.assertTrue(tongue_path.exists()) - - right_palm_path = self._get_output_filepath( - output_dir, 'bodysiteright palm') - self.assertTrue(right_palm_path.exists()) - - left_palm_path = self._get_output_filepath( - output_dir, 'bodysiteleft palm') - self.assertTrue(left_palm_path.exists()) - - # this feature's effect size is greater - # than the threshold only in tongue and left palm - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(tongue_path).read()) - self.assertFalse( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(right_palm_path).read()) - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(left_palm_path).read()) - - def test_filter_on_feature_ids(self): - ids_to_keep = ['bfbed36e63b69fec4627424163d20118', - '4b5eeb300368260019c1fbc7a3c718fc'] - - # confirm feature presence when no filtering - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf1.view(DataLoafPackageDirFmt), - feature_id_label='id', - feature_ids=None) - - tongue_path = self._get_output_filepath( - output_dir, 'bodysitetongue') - self.assertTrue(tongue_path.exists()) - - right_palm_path = self._get_output_filepath( - output_dir, 'bodysiteright palm') - self.assertTrue(right_palm_path.exists()) - - left_palm_path = self._get_output_filepath( - output_dir, 'bodysiteleft palm') - self.assertTrue(left_palm_path.exists()) - - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(tongue_path).read()) - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(right_palm_path).read()) - self.assertTrue( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(left_palm_path).read()) - - # confirm feature absence when filtering - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf1.view(DataLoafPackageDirFmt), - feature_id_label='id', - feature_ids=ids_to_keep) - - tongue_path = self._get_output_filepath( - output_dir, 'bodysitetongue') - self.assertTrue(tongue_path.exists()) - - right_palm_path = self._get_output_filepath( - output_dir, 'bodysiteright palm') - self.assertTrue(right_palm_path.exists()) - - left_palm_path = self._get_output_filepath( - output_dir, 'bodysiteleft palm') - self.assertTrue(left_palm_path.exists()) - - # feature ids expected to be absent are absent - self.assertFalse( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(tongue_path).read()) - self.assertFalse( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(right_palm_path).read()) - self.assertFalse( - 'd29fe3c70564fc0f69f2c03e0d1e5561' in - open(left_palm_path).read()) - - # feature ids expected to be present are present - self.assertTrue( - 'bfbed36e63b69fec4627424163d20118' in - open(tongue_path).read()) - self.assertTrue( - 'bfbed36e63b69fec4627424163d20118' in - open(right_palm_path).read()) - self.assertTrue( - 'bfbed36e63b69fec4627424163d20118' in - open(left_palm_path).read()) - - self.assertTrue( - '4b5eeb300368260019c1fbc7a3c718fc' in - open(tongue_path).read()) - self.assertTrue( - '4b5eeb300368260019c1fbc7a3c718fc' in - open(right_palm_path).read()) - self.assertTrue( - '4b5eeb300368260019c1fbc7a3c718fc' in - open(left_palm_path).read()) - - def test_error_on_bad_column_names(self): - with tempfile.TemporaryDirectory() as output_dir: - with self.assertRaisesRegex(KeyError, "id.*\"taxon\".*not"): - da_barplot(output_dir, - data=self.dataloaf1.view(DataLoafPackageDirFmt), - feature_id_label='taxon') - - with tempfile.TemporaryDirectory() as output_dir: - with self.assertRaisesRegex(KeyError, "label.*stderr.*not"): - da_barplot(output_dir, - data=self.dataloaf1.view(DataLoafPackageDirFmt), - error_label='stderr') - - def test_toggle_level_delimiter(self): - # no delimiter - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf2.view(DataLoafPackageDirFmt)) - - feces_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:feces') - self.assertTrue(feces_path.exists()) - - oral_cavity_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:oral cavity') - self.assertTrue(oral_cavity_path.exists()) - - saliva_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:saliva') - self.assertTrue(saliva_path.exists()) - - vagina_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:vagina') - self.assertTrue(vagina_path.exists()) - - # multi-level information should be present as 'y-label' - self.assertTrue( - '"y_label": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(feces_path).read()) - self.assertTrue( - '"y_label": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(oral_cavity_path).read()) - self.assertTrue( - '"y_label": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(saliva_path).read()) - self.assertTrue( - '"y_label": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(vagina_path).read()) - - # same labels should be present as 'feature' - self.assertTrue( - '"feature": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(feces_path).read()) - self.assertTrue( - '"feature": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(oral_cavity_path).read()) - self.assertTrue( - '"feature": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(saliva_path).read()) - self.assertTrue( - '"feature": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(vagina_path).read()) - - # typical delimiter: ; - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf2.view(DataLoafPackageDirFmt), - level_delimiter=';') - - feces_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:feces') - self.assertTrue(feces_path.exists()) - - oral_cavity_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:oral cavity') - self.assertTrue(oral_cavity_path.exists()) - - saliva_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:saliva') - self.assertTrue(saliva_path.exists()) - - vagina_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:vagina') - self.assertTrue(vagina_path.exists()) - - # single-level information should be present as 'y-label' - self.assertTrue( - '"y_label": "g__Staphylococcus' in - open(feces_path).read()) - self.assertTrue( - '"y_label": "g__Staphylococcus' in - open(oral_cavity_path).read()) - self.assertTrue( - '"y_label": "g__Staphylococcus' in - open(saliva_path).read()) - self.assertTrue( - '"y_label": "g__Staphylococcus' in - open(vagina_path).read()) - - # space delimited labels should be present as 'feature' - self.assertTrue( - '"feature": "d__Bacteria p__Firmicutes c__Bacilli o__Staphylococcales f__Staphylococcaceae g__Staphylococcus"' # noqa: E501 - in open(feces_path).read()) - self.assertTrue( - '"feature": "d__Bacteria p__Firmicutes c__Bacilli o__Staphylococcales f__Staphylococcaceae g__Staphylococcus"' # noqa: E501 - in open(oral_cavity_path).read()) - self.assertTrue( - '"feature": "d__Bacteria p__Firmicutes c__Bacilli o__Staphylococcales f__Staphylococcaceae g__Staphylococcus"' # noqa: E501 - in open(saliva_path).read()) - self.assertTrue( - '"feature": "d__Bacteria p__Firmicutes c__Bacilli o__Staphylococcales f__Staphylococcaceae g__Staphylococcus"' # noqa: E501 - in open(vagina_path).read()) - - # weird delimiter: __ - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf2.view(DataLoafPackageDirFmt), - level_delimiter='__') - - feces_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:feces') - self.assertTrue(feces_path.exists()) - - oral_cavity_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:oral cavity') - self.assertTrue(oral_cavity_path.exists()) - - saliva_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:saliva') - self.assertTrue(saliva_path.exists()) - - vagina_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:vagina') - self.assertTrue(vagina_path.exists()) - - # single-level information should be present as 'y-label' - self.assertTrue( - '"y_label": "Staphylococcus' in - open(feces_path).read()) - self.assertTrue( - '"y_label": "Staphylococcus' in - open(oral_cavity_path).read()) - self.assertTrue( - '"y_label": "Staphylococcus' in - open(saliva_path).read()) - self.assertTrue( - '"y_label": "Staphylococcus' in - open(vagina_path).read()) - - # space delimited labels should be present as 'feature' - self.assertTrue( - '"feature": "d Bacteria;p Firmicutes;c Bacilli;o Staphylococcales;f Staphylococcaceae;g Staphylococcus"' # noqa: E501 - in open(feces_path).read()) - self.assertTrue( - '"feature": "d Bacteria;p Firmicutes;c Bacilli;o Staphylococcales;f Staphylococcaceae;g Staphylococcus"' # noqa: E501 - in open(oral_cavity_path).read()) - self.assertTrue( - '"feature": "d Bacteria;p Firmicutes;c Bacilli;o Staphylococcales;f Staphylococcaceae;g Staphylococcus"' # noqa: E501 - in open(saliva_path).read()) - self.assertTrue( - '"feature": "d Bacteria;p Firmicutes;c Bacilli;o Staphylococcales;f Staphylococcaceae;g Staphylococcus"' # noqa: E501 - in open(vagina_path).read()) - - # missing delimiter: ! - with tempfile.TemporaryDirectory() as output_dir: - output_dir = Path(output_dir) - _ = da_barplot(output_dir, - self.dataloaf2.view(DataLoafPackageDirFmt), - level_delimiter='!') - - feces_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:feces') - self.assertTrue(feces_path.exists()) - - oral_cavity_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:oral cavity') - self.assertTrue(oral_cavity_path.exists()) - - saliva_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:saliva') - self.assertTrue(saliva_path.exists()) - - vagina_path = self._get_output_filepath( - output_dir, 'body_habitatUBERON:vagina') - self.assertTrue(vagina_path.exists()) - - # multi-level information should be present as 'y-label' - self.assertTrue( - '"y_label": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(feces_path).read()) - self.assertTrue( - '"y_label": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(oral_cavity_path).read()) - self.assertTrue( - '"y_label": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(saliva_path).read()) - self.assertTrue( - '"y_label": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(vagina_path).read()) - - # same labels should be present as 'feature' - self.assertTrue( - '"feature": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(feces_path).read()) - self.assertTrue( - '"feature": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(oral_cavity_path).read()) - self.assertTrue( - '"feature": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(saliva_path).read()) - self.assertTrue( - '"feature": "d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Staphylococcaceae;g__Staphylococcus"' # noqa: E501 - in open(vagina_path).read()) From 79701bedc6622471ecb6eecccf18f2869941ba9b Mon Sep 17 00:00:00 2001 From: Macabe Wood Date: Tue, 19 May 2026 14:19:29 -0700 Subject: [PATCH 05/15] lint --- q2_composition/plugin_setup.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/q2_composition/plugin_setup.py b/q2_composition/plugin_setup.py index e81fc78..0422454 100644 --- a/q2_composition/plugin_setup.py +++ b/q2_composition/plugin_setup.py @@ -8,8 +8,6 @@ import importlib -import numpy as np - from qiime2.plugin import (Int, Float, Bool, Str, List, Choices, Citations, Plugin, Metadata, MetadataColumn, Categorical, Range, Threads) @@ -305,7 +303,7 @@ }, name='Visualize ANCOMBC/ANCOMBC2 output.', description=( - 'Displays ANCOMBC/ANCOMBC2 Log-Fold Change values in a barplot and ' + 'Displays ANCOMBC/ANCOMBC2 Log-Fold Change values in a barplot and ' 'allows filtering based on p-value and standard error. If a taxonomy ' 'is provided, features can be filtered by taxonomy using an ' 'interactive tree.' From 9cd58b6e2b035f42850c0ba1e981d5d6b0f41003 Mon Sep 17 00:00:00 2001 From: Macabe Wood Date: Tue, 19 May 2026 14:27:43 -0700 Subject: [PATCH 06/15] renaming folder --- .../_ancombc2_visualizer/.gitignore | 26 - .../.vscode/extensions.json | 3 - .../_ancombc2_visualizer/index.html | 14 - .../_ancombc2_visualizer/package-lock.json | 4310 ----------------- .../_ancombc2_visualizer/package.json | 30 - .../_ancombc2_visualizer/src/App.svelte | 61 - .../_ancombc2_visualizer/src/app.css | 12 - .../src/lib/Barplot.svelte | 47 - .../src/lib/BarplotControls.svelte | 82 - .../src/lib/BarplotFilters.svelte | 157 - .../src/lib/ControlContainer.svelte | 8 - .../src/lib/SelectedTaxon.svelte | 147 - .../src/lib/Taxonomy.svelte | 37 - .../src/lib/TaxonomyFilter.svelte | 99 - .../src/lib/TaxonomyFilterList.svelte | 137 - .../_ancombc2_visualizer/src/main.ts | 9 - .../src/util/features.svelte.ts | 309 -- .../_ancombc2_visualizer/src/util/parse.ts | 148 - .../_ancombc2_visualizer/src/util/plot.ts | 526 -- .../src/util/taxonomy.svelte.ts | 729 --- .../_ancombc2_visualizer/src/vite-env.d.ts | 2 - 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-node_modules -dist -dist-ssr -*.local - -# Editor directories and files -.vscode/* -!.vscode/extensions.json -.idea -.DS_Store -*.suo -*.ntvs* -*.njsproj -*.sln -*.sw? - -!lib/ diff --git a/q2_composition/_ancombc2_visualizer/.vscode/extensions.json b/q2_composition/_ancombc2_visualizer/.vscode/extensions.json deleted file mode 100644 index bdef820..0000000 --- a/q2_composition/_ancombc2_visualizer/.vscode/extensions.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "recommendations": ["svelte.svelte-vscode"] -} diff --git a/q2_composition/_ancombc2_visualizer/index.html b/q2_composition/_ancombc2_visualizer/index.html deleted file mode 100644 index f9207c1..0000000 --- a/q2_composition/_ancombc2_visualizer/index.html +++ /dev/null @@ -1,14 +0,0 @@ - - - - - - - ANCOMBC2 Visualizer - - - -
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"name": "diverging-barplot", - "private": true, - "version": "0.0.0", - "type": "module", - "scripts": { - "dev": "vite", - "build": "vite build", - "preview": "vite preview", - "check": "svelte-check --tsconfig ./tsconfig.app.json && tsc -p tsconfig.node.json", - "test": "vitest" - }, - "devDependencies": { - "@sveltejs/vite-plugin-svelte": "^5.0.3", - "@tailwindcss/vite": "^4.1.4", - "@tsconfig/svelte": "^5.0.4", - "@types/d3": "^7.4.3", - "@types/node": "^22.10.5", - "svelte": "^5.53.0", - "svelte-check": "^4.1.1", - "tailwindcss": "^4.1.4", - "typescript": "~5.6.2", - "vite": "^6.4.1", - "vitest": "^2.1.8" - }, - "dependencies": { - "d3": "^7.9.0", - "ts-node": "^10.9.2" - } -} diff --git a/q2_composition/_ancombc2_visualizer/src/App.svelte b/q2_composition/_ancombc2_visualizer/src/App.svelte deleted file mode 100644 index 8099442..0000000 --- a/q2_composition/_ancombc2_visualizer/src/App.svelte +++ /dev/null @@ -1,61 +0,0 @@ - - -
- {#await featuresPromise} -

Parsing slices...

- {:then features} - - {:catch error} -

An error occurred: {error.message}

- {/await} - - {#await taxonomyPromise} -

Parsing taxonomy...

- {:then rootTaxon} - {#if rootTaxon} - - {/if} - {:catch error} -

An error occurred: {error.message}

- {/await} -
diff --git a/q2_composition/_ancombc2_visualizer/src/app.css b/q2_composition/_ancombc2_visualizer/src/app.css deleted file mode 100644 index 592a0a2..0000000 --- a/q2_composition/_ancombc2_visualizer/src/app.css +++ /dev/null @@ -1,12 +0,0 @@ -@import "tailwindcss"; - -button { - @apply px-4 py-1 bg-purple-500 text-white rounded cursor-pointer; -} -button:hover { - @apply bg-purple-600; -} - -button:active { - @apply bg-purple-700; -} \ No newline at end of file diff --git a/q2_composition/_ancombc2_visualizer/src/lib/Barplot.svelte b/q2_composition/_ancombc2_visualizer/src/lib/Barplot.svelte deleted file mode 100644 index 57ca1d6..0000000 --- a/q2_composition/_ancombc2_visualizer/src/lib/Barplot.svelte +++ /dev/null @@ -1,47 +0,0 @@ - - -
-
- {#if features.viewVariableLevel != ""} -

- Reference Level: {referenceLevel} -

- {/if} - -
- -
- - diff --git a/q2_composition/_ancombc2_visualizer/src/lib/BarplotControls.svelte b/q2_composition/_ancombc2_visualizer/src/lib/BarplotControls.svelte deleted file mode 100644 index 7bcdbf1..0000000 --- a/q2_composition/_ancombc2_visualizer/src/lib/BarplotControls.svelte +++ /dev/null @@ -1,82 +0,0 @@ - - - -
-
- - -
-
- - -
-
-

Bar Thickness:

- - -
-
- diff --git a/q2_composition/_ancombc2_visualizer/src/lib/BarplotFilters.svelte b/q2_composition/_ancombc2_visualizer/src/lib/BarplotFilters.svelte deleted file mode 100644 index 755f026..0000000 --- a/q2_composition/_ancombc2_visualizer/src/lib/BarplotFilters.svelte +++ /dev/null @@ -1,157 +0,0 @@ - - - -
-
- - -
-
- - -
-
- - -
- - - - {#if errorMessage} -

{errorMessage}

- {/if} -
- - -{#if filters.length} -
- {#each filters as filter} -
-

- {filter.slice} - {getSymbol(filter.relationship)} - {filter.value} -

- - -
- {/each} -
-{/if} - - diff --git a/q2_composition/_ancombc2_visualizer/src/lib/ControlContainer.svelte b/q2_composition/_ancombc2_visualizer/src/lib/ControlContainer.svelte deleted file mode 100644 index e50f5cf..0000000 --- a/q2_composition/_ancombc2_visualizer/src/lib/ControlContainer.svelte +++ /dev/null @@ -1,8 +0,0 @@ - - -
-

{title}

-
{@render children()}
-
diff --git a/q2_composition/_ancombc2_visualizer/src/lib/SelectedTaxon.svelte b/q2_composition/_ancombc2_visualizer/src/lib/SelectedTaxon.svelte deleted file mode 100644 index 861b2b2..0000000 --- a/q2_composition/_ancombc2_visualizer/src/lib/SelectedTaxon.svelte +++ /dev/null @@ -1,147 +0,0 @@ - - - -
- - -
- {#if searchError != ""} -
-

{searchError}

-
- {/if} -
- - -
-
- {#if taxonomyPlot?.selectedTaxon == undefined} - {#if searchError == ""} -

Click on a taxon name for more information.

- {/if} - {:else} -

Name: {name}

-

- Features classified to taxon: - {featureCount} ({featurePercent}%) -

-

- Features classified to subtree: - {subtreeCount} ({subtreePercent}%) -

- {/if} - - - diff --git a/q2_composition/_ancombc2_visualizer/src/lib/Taxonomy.svelte b/q2_composition/_ancombc2_visualizer/src/lib/Taxonomy.svelte deleted file mode 100644 index 2ee9f09..0000000 --- a/q2_composition/_ancombc2_visualizer/src/lib/Taxonomy.svelte +++ /dev/null @@ -1,37 +0,0 @@ - - -
-
- -
- -
- - diff --git a/q2_composition/_ancombc2_visualizer/src/lib/TaxonomyFilter.svelte b/q2_composition/_ancombc2_visualizer/src/lib/TaxonomyFilter.svelte deleted file mode 100644 index d8a5806..0000000 --- a/q2_composition/_ancombc2_visualizer/src/lib/TaxonomyFilter.svelte +++ /dev/null @@ -1,99 +0,0 @@ - - - -
-
- - -
-
- - -
- -
- - {#if errorMessage != ""} -
-

{errorMessage}

-
- {/if} - - - diff --git a/q2_composition/_ancombc2_visualizer/src/lib/TaxonomyFilterList.svelte b/q2_composition/_ancombc2_visualizer/src/lib/TaxonomyFilterList.svelte deleted file mode 100644 index 96f072b..0000000 --- a/q2_composition/_ancombc2_visualizer/src/lib/TaxonomyFilterList.svelte +++ /dev/null @@ -1,137 +0,0 @@ - - - -
- - -
-
- - -
-
- - -
-
- {#each taxonomyFilters?.filters as filter} -
- {#if filter.type == "feature-count"} -

features {"<"} {filter.value}

- - {:else if filter.type == "individual"} -

- individual filter of - {filter.node.getNonAnonymousTaxonString()} -

- - {/if} -
- {/each} -
- diff --git a/q2_composition/_ancombc2_visualizer/src/main.ts b/q2_composition/_ancombc2_visualizer/src/main.ts deleted file mode 100644 index 664a057..0000000 --- a/q2_composition/_ancombc2_visualizer/src/main.ts +++ /dev/null @@ -1,9 +0,0 @@ -import { mount } from 'svelte' -import './app.css' -import App from './App.svelte' - -const app = mount(App, { - target: document.getElementById('app')!, -}) - -export default app diff --git a/q2_composition/_ancombc2_visualizer/src/util/features.svelte.ts b/q2_composition/_ancombc2_visualizer/src/util/features.svelte.ts deleted file mode 100644 index b5b85a5..0000000 --- a/q2_composition/_ancombc2_visualizer/src/util/features.svelte.ts +++ /dev/null @@ -1,309 +0,0 @@ -import { TaxonomyNode } from "./taxonomy.svelte"; - -export type VariableRecord = { - name: string; - lfc?: number; - p?: number; - q?: number; - se?: number; - level?: string; - reference?: string; -} & Record; - -export class FeatureRecord { - featureId: string; - classification?: string; - shortClassification?: string; - variables: Map = new Map(); - - constructor(featureId: string, taxonomyNode?: TaxonomyNode) { - this.featureId = featureId; - - this.classification = taxonomyNode?.getFullTaxonString(); - if (taxonomyNode) { - const nonAnonymousName = taxonomyNode.getNonAnonymousTaxonString(); - this.shortClassification = `(${featureId.slice(0, 6)}) ${nonAnonymousName}`; - } - } - - /** - * Returns the variable with `variableName` and `level` or undefined if - * none is found. - */ - getVariable( - variableName: string, - level: string | undefined = undefined, - ): VariableRecord | undefined { - if (level) { - return this.variables.get(`${variableName}::${level}`); - } - - return this.variables.get(variableName); - } - - /** - * Creates a VariableRecord from primitives. - */ - createVariable( - variableName: string, - slice: string, - value: number, - level: string | undefined = undefined, - reference: string | undefined = undefined, - ): VariableRecord { - let variable = { - name: variableName, - [slice]: value, - }; - if (level && reference) { - variable.level = level; - variable.reference = reference; - } - - return variable; - } - - /** - * Adds a new variable to the set of feature variables. If a matching - * variable is already present then updates that variable with the any new - * slice properties from `variable`. - */ - addVariable(variable: VariableRecord): undefined { - let matchingVariable = this.getVariable(variable.name, variable.level); - - let newVariable: VariableRecord; - if (!matchingVariable) { - newVariable = variable; - } else { - newVariable = { - ...matchingVariable, - ...variable, - }; - } - - if (newVariable.level) { - this.variables.set( - `${newVariable.name}::${newVariable.level}`, - newVariable, - ); - } else { - this.variables.set(newVariable.name, newVariable); - } - } - - /** - * Returns the slice value for some variable. Errors if the variable or - * slice is not found. - */ - getVariableSlice( - variableName: string, - slice: string, - level: string | undefined = undefined, - ): number { - const variable = this.getVariable(variableName, level); - - if (!variable) { - throw new Error(`The ${variable} variable was not found.`); - } - if (!Object.hasOwn(variable, slice)) { - throw new Error(`The ${variable} variable has no ${slice} slice.`); - } - - return variable[slice] as number; - } -} - -export type ViewRecord = { - featureId: string; - lfc: number; - se: number; - p: number; - q: number; - classification: string; - shortClassification: string; -}; - -type Filter = { - (record: FeatureRecord): boolean; - slice: string; - relationship: string; - value: number; -}; - -export class FeatureRecords { - records: FeatureRecord[] = []; - - rootTaxon: TaxonomyNode | null = null; - hideFiltered: boolean = false; - showOnlyKept: boolean = false; - - view: ViewRecord[] = []; - viewVariable: string = $state(""); - viewVariableLevel: string = $state(""); - - filters: Filter[] = []; - - /** - * Returns an arbitrary variable record, useful for initializing the - * barplot. - */ - getInitialVariable(): VariableRecord { - return this.getAllVariables()[0]; - } - - /* - * Return the feature with id `featureId`, or undefined if not found. - */ - getFeature(featureId: string): FeatureRecord | undefined { - return this.records.find((r) => r.featureId == featureId); - } - - /** - * Adds a new feature. If a matching feature is already present then - * merges that feature's variables with those from `feature`. - */ - addFeature(feature: FeatureRecord): undefined { - let matchingFeature = this.getFeature(feature.featureId); - - if (!matchingFeature) { - this.records.push(feature); - } else { - Array.from(feature.variables.values()).forEach((v) => - matchingFeature.addVariable(v), - ); - } - } - - /** - * Adds a user-specified filter to the set of filters applied to the - * data. The filter function is annotated with each of this functions - * arguments for display in the UI. - */ - addFilter(slice: string, relationship: string, value: number) { - const filter = (record: FeatureRecord) => { - const variableValue = record.getVariableSlice( - this.viewVariable, - slice, - this.viewVariableLevel, - ); - - if (relationship == "gt") return variableValue > value; - if (relationship == "lt") return variableValue < value; - if (relationship == 'gtabsval') return Math.abs(variableValue) > value; - if (relationship == 'ltabsval') return Math.abs(variableValue) < value; - - throw new Error(`Unexpected relationship ${relationship}.`); - }; - - // annotate function with its defining characteristics - filter.slice = slice; - filter.relationship = relationship; - filter.value = value; - - this.filters.push(filter); - } - - /** - * Removes a filter by index. - */ - removeFilter(slice: string, relationship: string, value: number) { - this.filters = this.filters.filter((f) => { - return !( - f.slice == slice && - f.relationship == relationship && - f.value == value - ); - }); - } - - /** - * Returns all variable records in the feature dataset. Accessing only the - * first feature record is sufficient because all features have the same - * set of variable records. Removes the intercept variable record. - */ - getAllVariables(): VariableRecord[] { - const variables = Array.from(this.records[0].variables.values()); - return variables.filter((v) => v.name != "(Intercept)"); - } - - /** - */ - getVariablesWithName(variableName: string): VariableRecord[] { - const variables = this.getAllVariables(); - return variables.filter((v) => v.name == variableName); - } - - /** - * Renders the `view` by applying all existing filters, sorting features - * by decreasing lfc value, and extracting the slice values for the current - * `viewVariable`. - */ - render() { - let filtered: FeatureRecord[] = []; - - // apply taxonomyFilters if present - if (this.hideFiltered || this.showOnlyKept) { - for (let record of this.records) { - const node = this.rootTaxon.findTaxonById(record.featureId); - if (node == null) { - throw new Error( - `Could not find taxon with id ${record.featureId}`, - ); - } - - if (this.hideFiltered && !node.filtered) { - filtered.push(record); - } else if (this.showOnlyKept && node.hierarchyNode.keep) { - filtered.push(record); - } - } - } else { - filtered = this.records; - } - - // apply slice filters - for (let f of Object.values(this.filters)) { - filtered = filtered.filter(f); - } - - // map to view records by only selecting from variable of interest - let viewRecords: ViewRecord[] = filtered.map((record) => { - const variable = record.getVariable( - this.viewVariable, - this.viewVariableLevel, - ); - - if (!variable) { - throw new Error( - `Could not find variable ${this.viewVariable}.`, - ); - } - - let classification = record.classification; - if (classification == null) classification = "N/A"; - - return { - featureId: record.featureId, - lfc: variable.lfc!, - se: variable.se!, - p: variable.p!, - q: variable.q!, - classification, - shortClassification: record.shortClassification, - }; - }); - - // filter null lfc values - viewRecords = viewRecords.filter((r) => r.lfc != null); - - // sort view records by decreasing lfc - viewRecords = viewRecords.sort((r1, r2) => r2.lfc - r1.lfc); - - // update state - this.view = viewRecords; - } -} - -// global state -let features = new FeatureRecords(); -export default features; diff --git a/q2_composition/_ancombc2_visualizer/src/util/parse.ts b/q2_composition/_ancombc2_visualizer/src/util/parse.ts deleted file mode 100644 index cfbc06b..0000000 --- a/q2_composition/_ancombc2_visualizer/src/util/parse.ts +++ /dev/null @@ -1,148 +0,0 @@ -import { text } from "d3-fetch"; - -import { - FeatureRecords, - FeatureRecord, - type VariableRecord, -} from "./features.svelte"; - -import { TaxonomyNode } from "./taxonomy.svelte"; - -type JSONLHeaderField = { - name: string; - type: string | null; - missing: boolean; - title: string; - description: string; - extra: Record; -}; -type JSONLHeader = { - doctype: object; - direction: string; - style: string; - fields: JSONLHeaderField[]; -}; -type JSONLFeatureRecord = { - taxon: string; -} & Record; - -/** - * Parses slice data from the ANCOMBC2 output format that resides inside of the - * visualization artifact. Side-effects `featureRecords` by adding/updating - * parsed features. - */ -export async function parseAllSlices( - slicesDir: string, - featureRecords: FeatureRecords, - rootTaxon: TaxonomyNode | null = null, -): Promise { - const slices = ["lfc", "p", "q", "se"]; - for (let slice of slices) { - const sliceFilepath = `${slicesDir}/${slice}.jsonl`; - await parseSlice(sliceFilepath, featureRecords, rootTaxon); - } - - return Promise.resolve(); -} - -/** - * Parses a JSONL slice into `FeatureRecord`s and adds them to `featureRecords`. - */ -export async function parseSlice( - sliceFilepath: string, - featureRecords: FeatureRecords, - rootTaxon: TaxonomyNode | null, -): Promise { - // open file, convert to json - const textData: string = await text(sliceFilepath); - const jsonRecords: any = textData - .split("\n") - .filter((line) => line.trim() != "") - .map((line) => JSON.parse(line)); - - // parse header and check if empty - if (jsonRecords.length < 1) { - const msg = `The ${sliceFilepath} slice is empty.`; - throw new Error(msg); - } else if (jsonRecords.length === 1) { - const msg = `The ${sliceFilepath} slice has a header but no records.`; - throw new Error(msg); - } - const header: JSONLHeader = jsonRecords.shift()!; - - // parse each remaining line into a feature record - const jsonFeatureRecords: JSONLFeatureRecord[] = jsonRecords; - const sliceName = sliceFilepath.split("/").pop()!.replace(".jsonl", ""); - - jsonFeatureRecords.forEach((record) => { - const feature = parseJSONLFeatureRecord( - record, - header, - sliceName, - rootTaxon, - ); - featureRecords.addFeature(feature); - }); -} - -/** - * Parses a feature record line from a JSONL slice into a `FeatureRecord` - * object. - */ -export function parseJSONLFeatureRecord( - jsonRecord: JSONLFeatureRecord, - header: JSONLHeader, - slice: string, - rootTaxon: TaxonomyNode | null, -): FeatureRecord { - const taxonNode = rootTaxon?.findTaxonById(jsonRecord.taxon); - - const featureRecord = new FeatureRecord(jsonRecord.taxon, taxonNode); - - for (let column of Object.keys(jsonRecord)) { - if (column == "taxon") continue; - - const value = jsonRecord[column]; - - const headerField = getColumnField(column, header); - - let variable: VariableRecord; - if (headerField.extra.reference) { - variable = featureRecord.createVariable( - headerField.extra.variable, - slice, - value, - headerField.extra.level, - headerField.extra.reference, - ); - } else { - variable = featureRecord.createVariable(column, slice, value); - } - - featureRecord.addVariable(variable); - } - - return featureRecord; -} - -/** - * Retrieves the header field entry for the `column` column. - */ -export function getColumnField( - column: string, - header: JSONLHeader, -): JSONLHeaderField { - const columnFields: JSONLHeaderField[] = header.fields.filter((field) => { - return field.name === column; - }); - - if (columnFields.length > 1) { - const msg = `Duplicate name '${column}' found in JSONL header.`; - throw new Error(msg); - } else if (!columnFields.length) { - const msg = `Column ${column} not found in JSONL header.`; - throw new Error(msg); - } - - return columnFields.shift()!; -} diff --git a/q2_composition/_ancombc2_visualizer/src/util/plot.ts b/q2_composition/_ancombc2_visualizer/src/util/plot.ts deleted file mode 100644 index ef3a2e5..0000000 --- a/q2_composition/_ancombc2_visualizer/src/util/plot.ts +++ /dev/null @@ -1,526 +0,0 @@ -import * as d3 from "d3"; -import { type ViewRecord } from "./features.svelte"; - -type PlotDimensions = { - svgWidth: number; - svgHeight: number; - margin: number; - plotWidth: number; - plotHeight: number; - barHeight: number; - barPadding: number; -}; - -export class DivergingBarplot { - data: ViewRecord[] = []; - dimensions: PlotDimensions = {}; - xScale: d3.ScaleLinear = d3.scaleLinear(); - yScale: d3.ScaleBand = d3.scaleBand(); - xAxis: d3.Selection = d3.selection(); - yAxis: d3.Selection = d3.selection(); - - /** - */ - init(data: ViewRecord[]) { - this.data = data; - this.dimensions = this.createDimensions(); - this.xScale = this.createXScale(); - this.yScale = this.createYScale(); - this.xAxis = this.createXAxis(); - this.yAxis = this.createYAxis(); - } - - /** - */ - createDimensions(): PlotDimensions { - const svg = d3.select("svg"); - let svgWidth: number; - if (!svg.empty()) { - svgWidth = svg.node()!.getBoundingClientRect().width; - } else { - throw new Error(`Svg element not found.`); - } - - const numFeatures = this.data.length; - - const barHeight = 20; - const barPadding = 1.25; - - const plotHeight = numFeatures * barHeight * barPadding; - - const margin = 120; - const plotWidth = svgWidth - 2 * margin; - - return { - svgWidth: svgWidth, - svgHeight: plotHeight + 2 * margin, - margin, - plotWidth, - plotHeight, - barHeight, - barPadding, - }; - } - - /** - * Updates the plotted data and redraws the plot if the data is non-empty, - * otherwise hides the plot. - */ - updateData(data: ViewRecord[]) { - this.data = data; - if (data.length > 0) { - this.showPlot(); - this.drawPlot(true); - } else { - this.hidePlot(); - } - } - - /** - */ - updatePlotHeight() { - this.dimensions.plotHeight = - this.data.length * - this.dimensions.barHeight * - this.dimensions.barPadding; - this.dimensions.svgHeight = - this.dimensions.plotHeight + 2 * this.dimensions.margin; - } - - /** - */ - increaseBarThickness() { - this.dimensions.barHeight *= 1.1; - this.drawPlot(true); - } - - /** - */ - decreaseBarThickness() { - this.dimensions.barHeight *= 0.9; - this.drawPlot(true); - } - - /** - */ - getXDomain(): [number, number] { - // get min and max lfc +- se values - const lfc_minus_se = this.data.map((f) => f.lfc - f.se); - const lfc_plus_se = this.data.map((f) => f.lfc + f.se); - - let [min, max] = d3.extent([...lfc_minus_se, ...lfc_plus_se]); - - if (min == undefined || max == undefined) { - throw new Error("Unable to find min/max of feature lfcs."); - } - - // calculate scale range - const scaleMargin = 0.25; - if (min < 0) { - min = (1 + scaleMargin) * min; - } else { - min = -scaleMargin * max; - } - - if (max > 0) { - max = (1 + scaleMargin) * max; - } else { - max = -scaleMargin * min; - } - - return [min, max]; - } - - /** - */ - getXRange() { - return [ - this.dimensions.margin, - this.dimensions.margin + this.dimensions.plotWidth, - ]; - } - - /** - */ - createXScale(): d3.ScaleLinear { - const domain = this.getXDomain(); - const range = this.getXRange(); - const scale = d3.scaleLinear().domain(domain).range(range); - - return scale; - } - - /** - */ - getYDomain(): string[] { - return d3.range(0, this.data.length).map((i) => String(i)); - } - - /** - */ - getYRange() { - return [ - this.dimensions.margin, - this.dimensions.margin + this.dimensions.plotHeight, - ]; - } - - /** - */ - createYScale(): d3.ScaleBand { - const domain = this.getYDomain(); - const range = this.getYRange(); - const scale = d3.scaleBand().domain(domain).range(range); - - return scale; - } - - /** - */ - getXAxisTranslation() { - const translation = this.dimensions.margin + this.dimensions.plotHeight; - return `translate(0, ${translation})`; - } - - /** - */ - getYAxisTranslation() { - return `translate(${this.xScale(0)}, 0)`; - } - - /** - */ - createXAxis(): d3.Selection { - let axis = d3 - .select("svg") - .append("g") - .attr("class", "x-axis") - .attr("transform", this.getXAxisTranslation()) - .call(d3.axisBottom(this.xScale)); - - axis.selectAll("text").attr("font-size", "14px"); - - axis.append("text") - .text("LFC (Log Fold Change)") - .attr("fill", "black") - .attr("font-size", "18px") - .attr("id", "xaxis-label") - .attr("x", "50%") - .attr("y", 60); - - return axis; - } - - /** - */ - createYAxis(): d3.Selection { - let axis = d3 - .select("svg") - .append("g") - .attr("class", "y-axis") - .attr("transform", this.getYAxisTranslation()) - .call( - d3 - .axisLeft(this.yScale) - .tickSize(0) - .tickFormat("" as any), - ); - - return axis; - } - - /** - */ - addHoverHandlers() { - // event handlers - const handleMouseover = (e: any, d: any) => { - const tooltipData = [ - `feature ID: ${d.featureId}`, - `classification: ${d.classification}`, - `lfc: ${d.lfc}`, - `se: ${d.se}`, - `p-value: ${d.p}`, - `q-value: ${d.q}`, - ]; - - d3.select(".tooltip") - .style("display", "unset") - .style("left", `${e.clientX + 25}px`) - .style("top", `${e.clientY - 10}px`) - .selectAll("p") - .data(tooltipData) - .join("p") - .text((d, i) => tooltipData[i]) - .style("margin", "2px") - .style("box-shadow", "none"); - - d3.select(".tooltip") - .transition() - .duration(200) - .style("opacity", 1); - }; - - const handleMousemove = (e: any, d: any) => { - d3.select(".tooltip") - .style("left", `${e.clientX + 25}px`) - .style("top", `${e.clientY - 10}px`); - }; - - const handleMouseout = (e: any, d: any) => { - d3.select(".tooltip") - .transition() - .duration(200) - .style("opacity", 0) - .end() - .then(() => { - d3.select(".tooltip").style("display", "none"); - }); - }; - - // create tooltip - d3.select("body") - .selectAll(".tooltip") - .data([1]) - .join("div") - .attr("class", "tooltip") - .style("background-color", "#f0edef") - .style("padding", "10px") - .style("border-radius", "10px") - .style("position", "absolute") - .style("box-shadow", "1px 1px 2px gray") - .style("display", "none") - .style("opacity", 0); - - // register event handlers - d3.select("svg") - .selectAll("rect, .error-bar") - .on("mouseover", handleMouseover) - .on("mousemove", handleMousemove) - .on("mouseout", handleMouseout); - } - - /** - */ - drawErrorBar(path: d3.Path, d: ViewRecord, i: number): d3.Path { - // calculate error bar layout - const startX = this.xScale(d.lfc)!; - const startY = - this.yScale(i.toString())! + this.dimensions.barHeight / 2; - - const errorBarRight = this.xScale(d.lfc + d.se); - const errorBarLeft = startX - (errorBarRight - startX); - const errorBarTop = startY + 0.25 * this.dimensions.barHeight; - const errorBarBottom = startY - 0.25 * this.dimensions.barHeight; - - // draw error bar - path.moveTo(errorBarRight, errorBarTop); - path.lineTo(errorBarRight, errorBarBottom); - path.moveTo(errorBarRight, startY); - path.lineTo(errorBarLeft, startY); - path.moveTo(errorBarLeft, errorBarTop); - path.lineTo(errorBarLeft, errorBarBottom); - - return path; - } - - /** - */ - drawPlot(transition: boolean) { - const sizeSvg = () => { - let svg = d3 - .select("svg") - .attr("width", this.dimensions.svgWidth) - .attr("height", this.dimensions.svgHeight); - }; - - if (!transition) { - sizeSvg(); - } - - if (transition) { - // update plot height - this.updatePlotHeight(); - - // update scales - const xDomain = this.getXDomain(); - const xRange = this.getXRange(); - const yDomain = this.getYDomain(); - const yRange = this.getYRange(); - - this.xScale.domain(xDomain).range(xRange); - this.yScale.domain(yDomain).range(yRange); - - // resize svg - sizeSvg(); - - // transition axes - this.xAxis - .transition() - .duration(500) - .attr("transform", this.getXAxisTranslation()) - .call(d3.axisBottom(this.xScale)); - - this.xAxis.selectAll("text").attr("font-size", "14px"); - this.xAxis.select("#xaxis-label").attr("font-size", "18px"); - - this.yAxis - .transition() - .duration(500) - .attr("transform", this.getYAxisTranslation()) - .call( - d3 - .axisLeft(this.yScale) - .tickSize(0) - .tickFormat("" as any), - ); - } - - // draw bars - let barSelection = d3 - .select("svg") - .selectAll("rect") - .data(this.data) - .join("rect"); - - const drawBars = (selection: any) => { - selection - .attr("x", (d) => - d.lfc > 0 ? this.xScale(0) : this.xScale(d.lfc), - ) - .attr("y", (d, i) => this.yScale(String(i))) - .attr("width", (d) => - Math.abs(this.xScale(d.lfc) - this.xScale(0)), - ) - .attr("height", this.dimensions.barHeight) - .attr("fill", (d) => (d.lfc > 0 ? "green" : "red")); - }; - - if (transition) { - barSelection.transition().duration(400).call(drawBars.bind(this)); - } else { - barSelection.call(drawBars.bind(this)); - } - - // draw error bars - let errorBarSelection = d3 - .select("svg") - .selectAll(".error-bar") - .data(this.data) - .join("path") - .attr("class", "error-bar"); - - const drawErrorBars = (selection: any) => { - selection - .attr("d", (d, i) => - this.drawErrorBar(d3.path(), d, i).toString(), - ) - .attr("stroke", "black") - .attr("stroke-width", "2px"); - }; - - if (transition) { - errorBarSelection - .transition() - .duration(400) - .call(drawErrorBars.bind(this)); - } else { - errorBarSelection.call(drawErrorBars.bind(this)); - } - - // draw labels - let labelSelection = d3 - .select("svg") - .selectAll(".label") - .data(this.data) - .join("text") - .attr("class", "label"); - - const drawLabels = (selection: any) => { - selection - .text((d) => { - let classification = d.shortClassification - ? d.shortClassification - : d.featureId; - - if (classification.length > 30) { - classification = classification.slice(0, 25) + "(...)"; - } - - return classification; - }) - .attr("x", (d) => { - if (d.lfc > 0) { - return Math.min( - this.xScale(d.lfc - d.se), - this.xScale(0), - ); - } - return Math.max(this.xScale(d.lfc + d.se), this.xScale(0)); - }) - .attr( - "y", - (d, i) => - this.yScale(String(i)) + this.yScale.bandwidth() / 2, - ) - .attr("text-anchor", (d) => (d.lfc > 0 ? "end" : "start")) - .attr("dx", (d) => (d.lfc > 0 ? -8 : 8)) - .attr("dy", "1px") - .attr("font-size", "12px") - .attr("fill", "#474747"); - }; - - if (transition) { - labelSelection - .transition() - .duration(400) - .call(drawLabels.bind(this)); - } else { - labelSelection.call(drawLabels.bind(this)); - } - - // attach hover event listeners - this.addHoverHandlers(); - } - - /** - */ - hidePlot() { - // gray-out the plot - d3.select("svg") - .append("rect") - .attr("class", "hider") - .attr("width", this.dimensions.svgWidth) - .attr("height", this.dimensions.svgHeight) - .attr("fill", "gray") - .attr("opacity", 0.9); - - // add error message - d3.select("svg") - .append("rect") - .attr("class", "hider-text-box") - .attr("x", 0.3 * this.dimensions.svgWidth) - .attr("y", 0.4 * this.dimensions.svgHeight) - .attr("width", 0.4 * this.dimensions.svgWidth) - .attr("height", 0.2 * this.dimensions.svgHeight) - .attr("fill", "white"); - - d3.select("svg") - .append("text") - .attr("class", "hider-text") - .text("Oops! All features were filtered.") - .attr("x", this.dimensions.svgWidth / 2) - .attr("y", this.dimensions.svgHeight / 2) - .attr("dominant-baseline", "middle") - .attr("text-anchor", "middle") - .attr("font-size", "18px"); - } - - /** - */ - showPlot() { - d3.selectAll(".hider, .hider-text, .hider-text-box").remove(); - } -} - -const plot = new DivergingBarplot(); -export default plot; diff --git a/q2_composition/_ancombc2_visualizer/src/util/taxonomy.svelte.ts b/q2_composition/_ancombc2_visualizer/src/util/taxonomy.svelte.ts deleted file mode 100644 index d362f6d..0000000 --- a/q2_composition/_ancombc2_visualizer/src/util/taxonomy.svelte.ts +++ /dev/null @@ -1,729 +0,0 @@ -import { tsv } from "d3-fetch"; -import * as d3 from "d3"; - -type PlotDimensions = { - margin: number; - nodeWidth: number; - nodeHeight: number; - boxHeight: number; - boxWidth: number; -}; - -export class TaxonomyPlot { - dimensions: PlotDimensions; - root: d3.HierarchyNode; - treeLayout: d3.TreeLayout; - link: d3.Link; - - selectedTaxon: TaxonomyNode | null = $state(null); - hideFiltered: boolean = false; - - constructor(root: d3.HierarchyNode) { - this.root = root; - this.initTree(this.root); - - this.dimensions = this.getDimensions(); - this.treeLayout = this.createTreeLayout(); - this.link = this.createLinkGenerator(); - - this.initSvg(); - } - - initTree(root: d3.HierarchyNode) { - root.descendants().forEach((node, i) => { - node._children = node.children; - node.id = i; - node.children = null; - node.expand = false; - node.keep = false; - node.match = false; - }); - } - - getSvgDimensions() { - const svg = d3.select("#taxonomy-svg-container svg"); - - if (svg.empty()) { - throw new Error("No svg element found."); - } - - const svgRect = (svg.node() as any).getBoundingClientRect(); - - return { width: svgRect.width, height: svgRect.height }; - } - - getDimensions() { - const margin = 25; - - const { width: svgWidth, height: svgHeight } = this.getSvgDimensions(); - - const taxonomyDepth = this.root.height; - const nodeWidth = 225; - const nodeHeight = 30; - - const dimensions: PlotDimensions = { - margin: margin, - nodeHeight: nodeHeight, - nodeWidth: nodeWidth, - boxWidth: 0.8 * nodeWidth, - boxHeight: 0.8 * nodeHeight, - }; - - return dimensions; - } - - createTreeLayout(): d3.TreeLayout { - const treeLayout = d3 - .tree() - .nodeSize([this.dimensions.nodeHeight, this.dimensions.nodeWidth]); - - return treeLayout; - } - - createLinkGenerator(): d3.Link { - return d3 - .linkHorizontal() - .x((d) => d.y) - .y((d) => d.x); - } - - initSvg() { - const svg = d3.select("#taxonomy-svg-container svg"); - - // create groups for nodes and links - const zoomContainer = svg.append("g"); - zoomContainer.append("g").attr("class", "link-group"); - zoomContainer.append("g").attr("class", "node-group"); - - // set svg view box - const { width: svgWidth, height: svgHeight } = this.getSvgDimensions(); - - svg.attr("viewBox", [ - -this.dimensions.margin, - -svgHeight / 2, - svgWidth, - svgHeight, - ]); - - // make svg zoomable & pannable - const zoom = d3 - .zoom() - .scaleExtent([0.4, 2]) - .on("zoom", (event) => { - zoomContainer.attr("transform", event.transform); - }); - - svg.call(zoom).on("dblclick.zoom", null); - } - - addSelectHandlers() { - d3.selectAll(".taxonomy-node").on("click", (event, d) => { - this.selectedTaxon = d.data; - }); - } - - addExpandHandlers() { - d3.selectAll(".expand-button").on("click", (event, d) => { - d.expand = !d.expand; - this.render(d); - - event.stopPropagation(); - }); - } - - addKeepHandlers() { - d3.selectAll(".keep-button").on("click", (event, d) => { - d.keep = !d.keep; - - const fillColor = d.keep ? "orange" : "lightgray"; - d3.select(event.currentTarget) - .select("rect") - .attr("fill", fillColor); - - this.render(d); - - event.stopPropagation(); - }); - } - - drawButton( - selection: d3.Selection, - type: "expand" | "keep", - ) { - let xTranslation; - let className; - let letter; - if (type == "expand") { - xTranslation = this.dimensions.boxWidth - this.dimensions.boxHeight; - className = "expand-button"; - letter = "E"; - } else if (type == "keep") { - xTranslation = - this.dimensions.boxWidth - 2 * this.dimensions.boxHeight; - className = "keep-button"; - letter = "K"; - } else { - throw new Error("Unrecognized button type."); - } - - const button = selection - .append("g") - .attr("class", className) - .attr("transform", `translate(${xTranslation}, 2)`); - - button - .append("rect") - .attr("width", this.dimensions.boxHeight - 4) - .attr("height", this.dimensions.boxHeight - 4) - .attr("fill", "lightgray"); - - if (type == "keep") { - button - .selectAll("rect") - .attr("fill", (d) => (d.keep ? "orange" : "lightgray")); - } - - button - .append("text") - .text(letter) - .attr("x", this.dimensions.boxHeight / 2 - 2) - .attr("y", this.dimensions.boxHeight / 2 - 2) - .attr("dominant-baseline", "middle") - .attr("text-anchor", "middle") - .attr("font-size", 14) - .attr("dy", 2); - } - - drawNodes( - nodes: d3.HierarchyNode[], - source: d3.HierarchyNode, - ) { - const updateSelection = d3 - .select(".node-group") - .selectAll(".taxonomy-node") - .data(nodes, (d) => d.id); - - // create entering node groups - const enterSelection = updateSelection - .enter() - .append("g") - .attr("class", "taxonomy-node") - .attr("cursor", "pointer") - .attr("transform", (d) => `translate(${source.y0}, ${source.x0})`) - .attr("stroke-opacity", 1) - .attr("fill-opacity", 1); - - // taxon names - enterSelection - .append("text") - .text((d) => { - if (d.data.name.length > 18) { - return d.data.name.slice(0, 15) + "..."; - } - return d.data.name; - }) - .attr("dx", 10) - .attr("y", this.dimensions.boxHeight / 2) - .attr("dominant-baseline", "middle") - .attr("stroke-linejoin", "round") - .attr("stroke-width", 5) - .attr("stroke", "white") - .attr("paint-order", "stroke") - .attr("font-weight", "bold") - .attr("font-size", 13); - - // draw taxon boxes - enterSelection - .append("rect") - .attr("class", "taxon-box") - .attr("height", this.dimensions.boxHeight) - .attr("width", this.dimensions.boxWidth) - .attr("fill", (d) => { - if (d.data.searchMatch) return "green"; - if (d.data.filtered) return "red"; - return "white"; - }) - .attr("stroke", "gray") - .attr("stroke-width", 2) - .attr("rx", 2) - .attr("ry", 2) - .attr("stroke-opacity", 1) - .attr("fill-opacity", (d) => { - if (d.data.searchMatch || d.data.filtered) { - return 0.2; - } - return 0; - }); - - // left circle - enterSelection - .append("circle") - .attr("cx", 0) - .attr("cy", this.dimensions.boxHeight / 2) - .attr("r", 3) - .attr("fill", "#555"); - - // right circle; visible only if node has children - enterSelection - .append("circle") - .attr("class", "right-circle") - .attr("cx", this.dimensions.boxWidth) - .attr("cy", this.dimensions.boxHeight / 2) - .attr("r", (d) => { - let kept = d._children; - if (this.hideFiltered) { - kept = d._children?.filter((n) => !n.data.filtered); - } - if (kept && kept.length > 0) { - return 3; - } - return 0; - }) - .attr("fill", "#555"); - - updateSelection.selectAll(".right-circle").attr("r", (d) => { - let kept = d._children; - if (this.hideFiltered) { - kept = d._children?.filter((n) => !n.data.filtered); - } - if (kept && kept.length > 0) { - return 3; - } - return 0; - }); - - // color search matches - updateSelection - .selectAll(".taxon-box") - .attr("fill", (d) => { - if (d.data.searchMatch) return "green"; - if (d.data.filtered) return "red"; - return "white"; - }) - .attr("fill-opacity", (d) => { - if (d.data.searchMatch || d.data.filtered) { - return 0.2; - } - return 0; - }); - - this.drawButton(enterSelection, "expand"); - this.drawButton(enterSelection, "keep"); - - // add click event handlers - this.addSelectHandlers(); - this.addExpandHandlers(); - this.addKeepHandlers(); - - // color buttons - updateSelection - .merge(enterSelection) - .selectAll(".expand-button") - .select("rect") - .attr("fill", (d) => { - if (d.children && d.children.length == d._children.length) { - return "lightblue"; - } else { - return "lightgray"; - } - }); - - updateSelection - .merge(enterSelection) - .selectAll(".keep-button") - .select("rect") - .attr("fill", (d) => (d.keep ? "orange" : "lightgray")); - - // transition all nodes to their new positions - updateSelection - .merge(enterSelection) - .transition() - .duration(200) - .attr("transform", (d) => `translate(${d.y}, ${d.x})`) - .attr("fill-opacity", 1) - .attr("stroke-opacity", 1); - - // transition exiting nodes to parents' new positions - updateSelection - .exit() - .transition() - .duration(200) - .remove() - .attr("transform", (d) => `translate(${source.y}, ${source.x})`) - .attr("fill-opacity", 0) - .attr("stroke-opacity", 0); - } - - drawLinks( - links: d3.HierarchyLink[], - source: d3.HierarchyNode, - ) { - const updateSelection = d3 - .select(".link-group") - .selectAll(".taxonomy-link") - .data(links, (d) => d.target.id); - - // create entering link paths - const enterSelection = updateSelection - .enter() - .append("path") - .attr("class", "taxonomy-link") - .attr("fill", "none") - .attr("stroke", "#555") - .attr("stroke-opacity", 0.5) - .attr("stroke-width", 1.5) - .attr("d", (d) => { - const parentOld = { x: source.x0, y: source.y0 }; - return this.link({ source: parentOld, target: parentOld }); - }); - - // transition all links to their new shapes - updateSelection - .merge(enterSelection) - .transition() - .duration(200) - .attr("d", (d) => { - const sourceX = d.source.x! + this.dimensions.boxHeight / 2; - const targetX = d.target.x! + this.dimensions.boxHeight / 2; - - const sourceY = d.source.y! + this.dimensions.boxWidth; - const targetY = d.target.y!; - - const positions = { - source: { x: sourceX, y: sourceY }, - target: { x: targetX, y: targetY }, - }; - return this.link(positions); - }); - - // transition exiting links to parent's new position - updateSelection - .exit() - .transition() - .duration(200) - .remove() - .attr("d", (d) => { - const parentNew = { x: source.x, y: source.y }; - return this.link({ source: parentNew, target: parentNew }); - }); - } - - assignChildren(node: d3.HierarchyNode): boolean { - let keptDescendant = node.keep || node.data.searchMatch; - - if (this.hideFiltered && node.data.filtered) { - return false; - } - - // leaf - if (!node._children) { - return keptDescendant; - } - - node.children = []; - for (let child of node._children) { - if (this.assignChildren(child)) { - node.children.push(child); - keptDescendant = true; - } - } - - if (node.expand) { - node.children = node._children; - if (this.hideFiltered) { - node.children = node.children.filter((n) => !n.data.filtered); - } - } - - if (node.children!.length == 0) { - node.children = undefined; - } - - return keptDescendant; - } - - render(source: d3.HierarchyNode) { - // update visible children - this.assignChildren(this.root); - - // gather all expanded nodes and links - const nodes = this.root.descendants().reverse(); - const links = this.root.links(); - - // assign coordinates to nodes - this.treeLayout(this.root); - - // const transition = this.resizeSvg(); - this.drawLinks(links, source); - this.drawNodes(nodes, source); - - // store the current positions for the next render - this.root.eachBefore((node) => { - node.x0 = node.x; - node.y0 = node.y; - }); - } -} - -export class TaxonomyNode { - name: string; - parent: TaxonomyNode | null; - children: TaxonomyNode[]; - featureIDs: string[]; - hierarchyNode: d3.HierarchyNode | null; - searchMatch: boolean = false; - filtered: boolean = false; - - constructor(name: string, parent: TaxonomyNode | null) { - this.name = name; - this.parent = parent; - this.children = []; - this.featureIDs = []; - this.hierarchyNode = null; - } - - getChild(name: string): TaxonomyNode | null { - let matchingChildren = this.children.filter((child) => { - return child.name == name; - }); - - if (matchingChildren.length > 1) { - throw new Error("More than one matching child found."); - } - if (matchingChildren.length == 0) { - return null; - } - - return matchingChildren[0]; - } - - getRoot(): TaxonomyNode { - let currentNode: TaxonomyNode = this; - while (currentNode.parent != null) { - currentNode = currentNode.parent; - } - - return currentNode; - } - - getDescendants(): TaxonomyNode[] { - const descendants: TaxonomyNode[] = [this]; - for (let child of this.children) { - descendants.push(...child.getDescendants()); - } - - return descendants; - } - - findTaxa(name: string): TaxonomyNode[] { - const root = this.getRoot(); - const descendants = root.getDescendants(); - - const matches = descendants.filter((descendant) => { - const index = descendant.name - .toLowerCase() - .indexOf(name.toLowerCase()); - - return index != -1 && !descendant.filtered; - }); - - return matches; - } - - findTaxonById(id: string): TaxonomyNode | null { - const descendants = this.getRoot().getDescendants(); - const matches = descendants.filter((descendant) => { - return descendant.featureIDs.indexOf(id) != -1; - }); - - if (matches.length == 0) { - return null; - } else if (matches.length == 1) { - return matches[0]; - } else { - throw new Error( - "More than one taxonomy node with the same feature ID.", - ); - } - } - - getAncestors(): TaxonomyNode[] { - const ancestors = []; - let currentNode: TaxonomyNode = this; - while (currentNode.parent != null) { - ancestors.push(currentNode); - currentNode = currentNode.parent; - } - - return ancestors; - } - - getFullTaxonString(): string { - const ancestorNames = this.getAncestors() - .reverse() - .map((a) => a.name); - - return ancestorNames.join(";"); - } - - /** - * Gets the shortest taxonomy string that contains a non-anonymous level - * label. - * - * Examples: - * (...);f__family;g__genus;s__ => g__genus;s__ - * (...);o__order;f__family;g__;s__ => f__family;g__;s__ - * (...);g__genus;s__species => s__species - */ - getNonAnonymousTaxonString(): string { - if (this.parent == null) return "root"; - - const ancestorNames = this.getAncestors() - .reverse() - .map((a) => a.name); - - let lastNonAnonymousIndex = null; - for (const [index, ancestorName] of ancestorNames.entries()) { - if (ancestorName.slice(-2) != "__") { - lastNonAnonymousIndex = index; - } - } - if (lastNonAnonymousIndex == null) lastNonAnonymousIndex = 0; - - return ancestorNames.slice(lastNonAnonymousIndex).join(";"); - } - - getFeatureCount(): number { - return this.featureIDs.length; - } - - getSubtreeFeatureCount(): number { - let subtreeCount = this.getFeatureCount(); - - for (let child of this.children) { - subtreeCount += child.getSubtreeFeatureCount(); - } - - return subtreeCount; - } - - getTreeFeatureCount(): number { - return this.getRoot().getSubtreeFeatureCount(); - } - - clearSearchMatches() { - this.getRoot() - .getDescendants() - .forEach((n) => { - n.searchMatch = false; - }); - } -} - -export class TaxonomyFilters { - filters: ((node: TaxonomyNode) => boolean)[] = $state([]); - taxonomyRoot: TaxonomyNode; - - constructor(taxonomyRoot: TaxonomyNode) { - this.filters = []; - this.taxonomyRoot = taxonomyRoot; - } - - addFeatureCountFilter(featureCount: number) { - const filter = (node: TaxonomyNode) => { - return node.getSubtreeFeatureCount() < featureCount; - }; - - filter.type = "feature-count"; - filter.value = featureCount; - - this.filters = [...this.filters, filter]; - } - - removeFeatureCountFilter(value: number) { - this.filters = this.filters.filter((f) => { - if (f.type != "feature-count") return true; - - return !(f.value == value); - }); - } - - addIndividualFilter(filterNode: TaxonomyNode) { - const filter = (node: TaxonomyNode) => { - return node == filterNode; - }; - - filter.type = "individual"; - filter.node = filterNode; - - this.filters = [...this.filters, filter]; - } - - removeIndividualFilter(filterNode: TaxonomyNode) { - this.filters = this.filters.filter((f) => { - if (f.type != "individual") return true; - - return !(f.node == filterNode); - }); - } - - applyFilters() { - const nodes = this.taxonomyRoot.getDescendants(); - - nodes.forEach((node) => (node.filtered = false)); - - nodes.forEach((node) => { - for (let filter of this.filters) { - node.filtered = filter(node); - if (node.filtered) return; - } - }); - } -} - -/** - * Parses a taxonomy.tsv file into a d3.hierarchy. - */ -export async function parseTaxonomy( - taxonomyFilepath: string, -): Promise> { - const taxonomyRecords = await tsv(taxonomyFilepath); - - const root = new TaxonomyNode("root", null); - - for (let taxonRecord of taxonomyRecords) { - const levelNames = taxonRecord["Taxon"] - .split(";") - .filter((n) => n != ""); - const featureId = taxonRecord["Feature ID"]; - - let parentNode = root; - for (let [levelIndex, levelName] of levelNames.entries()) { - const currentNode = new TaxonomyNode(levelName, parentNode); - - // if this is the last level then it has a feature ID - if (levelIndex == levelNames.length - 1) { - currentNode.featureIDs.push(featureId); - } - - // merge with matching child if one exists - const matchingChild = parentNode.getChild(levelName); - if (matchingChild) { - matchingChild.featureIDs.push(...currentNode.featureIDs); - parentNode = matchingChild; - } else { - parentNode.children.push(currentNode); - parentNode = currentNode; - } - } - } - - const hierarchyRoot = d3.hierarchy(root); - - // create back references from TaxonomyNodes to d3 nodes - hierarchyRoot.eachBefore((node) => { - node.data.hierarchyNode = node; - }); - - return hierarchyRoot; -} diff --git a/q2_composition/_ancombc2_visualizer/src/vite-env.d.ts b/q2_composition/_ancombc2_visualizer/src/vite-env.d.ts deleted file mode 100644 index 4078e74..0000000 --- a/q2_composition/_ancombc2_visualizer/src/vite-env.d.ts +++ /dev/null @@ -1,2 +0,0 @@ -/// -/// diff --git a/q2_composition/_ancombc2_visualizer/svelte.config.js b/q2_composition/_ancombc2_visualizer/svelte.config.js deleted file mode 100644 index b0683fd..0000000 --- a/q2_composition/_ancombc2_visualizer/svelte.config.js +++ /dev/null @@ -1,7 +0,0 @@ -import { vitePreprocess } from '@sveltejs/vite-plugin-svelte' - -export default { - // Consult https://svelte.dev/docs#compile-time-svelte-preprocess - // for more information about preprocessors - preprocess: vitePreprocess(), -} diff --git a/q2_composition/_ancombc2_visualizer/tests/data/output-format/W.jsonl b/q2_composition/_ancombc2_visualizer/tests/data/output-format/W.jsonl deleted file mode 100644 index b2b60e3..0000000 --- a/q2_composition/_ancombc2_visualizer/tests/data/output-format/W.jsonl +++ /dev/null @@ -1,9 +0,0 @@ -{"doctype":{"name":"table.jsonl","format":"application/x-json-lines","version":"1.0"},"direction":"row","style":"key:value","fields":[{"name":"taxon","type":null,"missing":false,"title":"","description":"","extra":{}},{"name":"(Intercept)","type":null,"missing":false,"title":"","description":"","extra":{}},{"name":"body-site::left palm","type":null,"missing":false,"title":"","description":"","extra":{"variable":"body-site","level":"left palm","reference":"gut"}},{"name":"body-site::right palm","type":null,"missing":false,"title":"","description":"","extra":{"variable":"body-site","level":"right palm","reference":"gut"}},{"name":"body-site::tongue","type":null,"missing":false,"title":"","description":"","extra":{"variable":"body-site","level":"tongue","reference":"gut"}},{"name":"year","type":null,"missing":false,"title":"","description":"","extra":{}}],"index":[],"title":"","description":"","extra":{}} -{"taxon":"4b5eeb300368260019c1fbc7a3c718fc","(Intercept)":-1235411664.1230688095,"body-site::left palm":15.5292100831,"body-site::right palm":10.7105143567,"body-site::tongue":8.3444601801,"year":90816.4971581012} -{"taxon":"fe30ff0f71a38a39cf1717ec2be3a2fc","(Intercept)":-861683502.712356925,"body-site::left palm":12.8611438894,"body-site::right palm":20.1786232328,"body-site::tongue":-1.1898355664,"year":83819.0848453717} -{"taxon":"868528ca947bc57b69ffdf83e6b73bae","(Intercept)":-961414485.8867735863,"body-site::left palm":16.4795912965,"body-site::right 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a/q2_composition/_ancombc2_visualizer/tests/data/taxonomy.tsv +++ /dev/null @@ -1,771 +0,0 @@ -Feature ID Taxon Confidence -4b5eeb300368260019c1fbc7a3c718fc k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__ 0.9958337221946401 -fe30ff0f71a38a39cf1717ec2be3a2fc k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__; s__ 0.9999428120610714 -d29fe3c70564fc0f69f2c03e0d1e5561 k__Bacteria; p__Firmicutes; c__Bacilli; o__Lactobacillales; f__Streptococcaceae; g__Streptococcus; s__ 0.9999999999436398 -868528ca947bc57b69ffdf83e6b73bae k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__ 0.9664365168086811 -154709e160e8cada6bfb21115acc80f5 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__ 0.9786399509952004 -1d2e5f3444ca750c85302ceee2473331 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales; f__Pasteurellaceae; g__Gallibacterium; s__ 0.9959925193403045 -0305a4993ecf2d8ef4149fdfc7592603 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__uniformis 0.9997327263589151 -cb2fe0146e2fbcb101050edb996a0ee2 k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Bacillaceae; g__Bacillus; s__cereus 0.8845609942227217 -997056ba80681bbbdd5d09aa591eadc0 k__Bacteria; p__Fusobacteria; c__Fusobacteriia; o__Fusobacteriales; f__Fusobacteriaceae; g__Fusobacterium; s__ 0.982050953447081 -3c9c437f27aca05f8db167cd080ff1ec k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 0.994133246661797 -9079bfebcce01d4b5c758067b1208c31 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__ 0.7046607060653575 -bfbed36e63b69fec4627424163d20118 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; 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0.99330596140401 -047b7fb62a5e9d2711e639ae1cb1519a k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Veillonellaceae; g__Dialister; s__ 0.9237938938176441 -0160e14a78b18b903618f11bc732746e k__Bacteria; p__Verrucomicrobia; c__Verrucomicrobiae; o__Verrucomicrobiales; f__Verrucomicrobiaceae; g__Akkermansia; s__muciniphila 0.9999999999958362 -e7c8b8c8fced8eead4b767bffe6dd544 k__Bacteria; p__Fusobacteria; c__Fusobacteriia; o__Fusobacteriales; f__Fusobacteriaceae; g__Fusobacterium; s__ 0.9999939317546679 -d2613a43f4ed1dda8a673e7fb251ebef k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Lachnospira; s__ 0.9999997755760827 -e31b5affbe5e23b79a8619589f3b6620 k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__ 0.9999999990585735 -7dd9c9124ec3f118a6cef1f0d422c011 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.742295742136374 -67e23140639733766b7e127f50221289 k__Bacteria; 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o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__ 0.9999999202641409 -469e4ff2129066178b74b112829fc03c k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__ 0.9999966339634149 -6edca9464612efff71d8f97299f01663 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 0.9888368635892377 -41fedaa9200e2933821f84ecdc0b0772 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Blautia; s__ 0.9998288585755445 -41735c13fb7f63db49b10fba5d959ce3 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; f__Neisseriaceae; g__; s__ 0.9999922527995685 -54d098d009b89779530eaf43a1bb136a k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pasteurellales; f__Pasteurellaceae; g__; s__ 0.9841307620937348 -76174505aef45f134d8068d5ad2c42aa k__Bacteria; p__Fusobacteria; c__Fusobacteriia; o__Fusobacteriales; f__Fusobacteriaceae; g__Cetobacterium; s__somerae 0.999989065299615 -b8afb7bb30b7a9170b7c6dcd40251d54 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.7910683742822175 -4c4606a3dbb4f5b8bb1ad1db6dfc5617 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__acnes 0.9814623426752663 -3ef461f213bfc675ddf0b1bfeef2dc52 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Alcaligenaceae; g__Sutterella; s__ 0.9348931942522047 -1f50ac250618ced095a2a5c34bae7651 k__Bacteria; p__Proteobacteria; c__Epsilonproteobacteria; o__Campylobacterales; f__Campylobacteraceae; g__Campylobacter; s__ 0.9998667199514364 -b3d4d129c955517b446df657236ba5a2 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__[Paraprevotellaceae] 0.7452402307199099 -fc15824cd9e9c29e1319d32843452b54 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfovibrionales; f__Desulfovibrionaceae; g__Desulfovibrio; s__ 0.9993291130018358 -f8f937eeee7762f446a0e87292f98eb6 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Parabacteroides; s__gordonii 0.9753745095429026 -b2866fdca13681232057e3e85a1978cf k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__ 0.9997867752403777 -052128d7d424728578efe7852b0afd0d k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.9763024906230429 -fc5b641a0b0408d99ddfb2a5ba64da59 k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__ 0.9999999961057711 -2514cdaab96a1a42cf15506f2ecf6439 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.8498350234496956 -e0472171de6fa02a1f58e392ad3d000e k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__ 0.9999999994890345 -e063d1c3c9daf7390e5475e48d9b01c5 k__Bacteria; p__Firmicutes; 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f__Pasteurellaceae; g__; s__ 0.8200457533405936 -880968796af86b3d6270c228fe8e7026 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae 0.9745304212780819 -81351ef6b4d49a3a6b2fc24745d70305 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria 0.999700105283307 -c4aad64f84f51ff331b986a67af4ed3d k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Moraxellaceae; g__Acinetobacter; s__ 0.9999641113701946 -79dcabe7f92f8cf2723b796dcd2f239f k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__ 0.9999999979512069 -7a5d5e6f85da7ca91daa2d803e8f9279 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Bacteroidaceae; g__Bacteroides; s__uniformis 0.8457322210944457 -401d7866836c54f3cd18bd0fc814885e k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Anaerococcus; s__ 0.9999999100598598 -75258a676bcd7e73c2437d6a2012d490 k__Bacteria; 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0.872880524507011 -a4c08e2c3a34038ea877b16d01736837 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.9406211885029296 -4075a90811bf9c19f02f5aa2ece6da37 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria 0.9862076771441829 -4980b85712efeef1fc4563a9a949fe2e k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__ 0.9999999943268136 -f91c81859bf6eede55eef9c915dd8bab k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.99970078019132 -5601f094afc823d75ccb34440645a99e k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Actinomycetaceae; g__Actinomyces; s__ 0.9906224971027953 -21a0198d0a83a8f3ec0e401067138940 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__Oscillospira; s__ 0.9008452096264863 -56c98126dde3abb2d263088db55e12c8 k__Bacteria; p__Bacteroidetes; c__Sphingobacteriia; o__Sphingobacteriales; f__Sphingobacteriaceae; g__; s__ 0.9999683646177029 -a659784c026bd9c8cde94da36aa656d7 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__Prevotella; s__ 0.9999993456027748 -f16a387e898dbae6432b2ed0241120bd k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Lachnospira; s__ 0.9995424783284206 -3125abe90c7ae91aec06eb104d71845f k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Anaerococcus; s__ 0.9999999999999787 -b383ade799e9c83c649cec37705a251d k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae 0.7462757768512205 -3bf2fc236887eda11c969b84d30f9fbf k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae; g__; s__ 0.9747187767070731 -3cdd97ba69a504117de24626ba790e96 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria 0.8770533277033848 -4132561a08d25757e4bee9f73ec4a70a k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Neisseriales; 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g__Parabacteroides; s__gordonii 0.990490233614371 -b1e22f094d8c64fb56dbacf680dab8c9 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae; g__Porphyromonas; s__ 0.99999991340653 -b92e89d105e0a6e09e5984879c4c7809 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Veillonellaceae; g__Megamonas; s__ 0.9998429390456497 -a5df9a825c3d8eeb228a6781c3db134c k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 0.9986964429534421 -ff3df50eea7490dd794148649c480fd3 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__; s__ 0.9686046064191691 -3a1c2d5547ddb7f76306a042f8bef6a4 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Oxalobacteraceae; g__; s__ 0.9179253970562418 -8da02c7114ba0d9ee40312926e037a8f k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Corynebacteriaceae; g__Corynebacterium; s__ 0.9999998866139841 -87899779aec8d38dfaf48d895cfe8021 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p__Proteobacteria; c__Epsilonproteobacteria; o__Campylobacterales; f__Campylobacteraceae; g__Campylobacter; s__ 0.9976261105781868 -51588a76b68ff3041e8b272256df5ae2 k__Bacteria; p__Synergistetes; c__Synergistia; o__Synergistales; f__Dethiosulfovibrionaceae; g__TG5; s__ 0.9070807368354143 -a3dc97e11838f1bf157aa875f2f6367d k__Bacteria; p__Bacteroidetes 0.9999999055295461 -f351326f9505ffc18da207391818c48e k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodobacterales; f__Rhodobacteraceae; g__; s__ 0.9821277811324446 -53dd9f9a89854c8ebdcfb105b7a26df1 k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Nocardioidaceae; g__; s__ 0.9991536366666571 -fbf110ef5de76f86121c8504a0cb786e k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 0.9465733411849421 -f66effc279917d65747b7c3ef8d62432 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__ 0.8328144562379329 -5c541619c0a084c6609e071895d9de55 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g__; s__ 0.790311130955446 -e54bcf1c8ec24811e7c355b8d82fa59e k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Nocardioidaceae; g__; s__ 0.9999999890900001 -cee164362eb3296a3d29e33f7b479d2e k__Bacteria; p__Cyanobacteria; c__; o__; f__; g__; s__ 0.8789686234635555 -71e9ece7818452114b1e87f8145aefd5 k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Porphyromonadaceae 0.8132539537195868 -ae4c61e598c093caa5b66b6919f02ba3 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhizobiales; f__Hyphomicrobiaceae; g__; s__ 0.9418486227376394 -a54095a893fd5abc045d162bbe20644a k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Comamonadaceae 0.908486538016183 -3253177a44672689e4e154e842d63e35 k__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales 0.9971138922337394 -45c36b8b2965484407b8b213419d4c6c k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae]; g__Anaerococcus; s__ 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0.985995667905748 -eed50a4877de2fd21b146b4f0c7327ac k__Bacteria; p__Chloroflexi; c__Gitt-GS-136; o__; f__; g__; s__ 0.7923905965393132 -6d7d9658988c6e2b5e45ea087f1b9155 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Mogibacteriaceae]; g__Mogibacterium; s__ 0.9999530128058945 -502b6544978890cda2ece2d14bfdba01 k__Bacteria 0.9999992713823516 -ca08eabd09756731f095632656d45b01 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; g__; s__ 0.9983619317607827 -694caec8dad781d338acf4a5b69c3058 k__Bacteria; p__Firmicutes; c__Erysipelotrichi; o__Erysipelotrichales; f__Erysipelotrichaceae; g__Allobaculum; s__ 0.9933864641518518 -14e1a93cf2379225b1fd6ed0f186bacb k__Bacteria; p__FBP; c__; o__; f__; g__; s__ 0.9996710419708875 -6488fe0aaa024ba9c06647578b5a6caf k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodospirillales; f__Acetobacteraceae; g__Roseococcus; s__ 0.9995620152418827 -5ce3a51e54f30fa53b1e56dc64d11340 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales 0.9951843239239426 -4d987a66ee0e67b68c5c4428097eb22e k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Thiotrichales; f__Thiotrichaceae; g__CF-26; s__ 0.7994705971955715 -c3fd5b1d03591477953d49f0f19600c4 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfovibrionales; f__Desulfomicrobiaceae; g__; s__ 0.9999999993020481 -08bd73939f7bfd85daf2eaee7e9c9bf8 Unassigned 0.8664133093465773 -93a769a6b67e5f358eb9ad0e03c53ec3 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Tissierellaceae] 0.9989722925004496 -654f282fc504b4dc9af5b8e66a4d1a87 k__Bacteria; p__GN02; c__BD1-5; o__; f__; g__; s__ 0.8937638443300449 -895453b352ae060e0ec5f7721547a3d1 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 0.7756571434765006 -b29143b255f4b97da62310d85fe9b7f3 k__Bacteria; p__Firmicutes; c__Clostridia 0.7084783782168641 -95dff3e66b8bdf4d8e509ceae4373c69 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Lachnospiraceae; g__Lachnospira; s__ 0.9997983395343405 -da3328e15aae60ea55a8765511d0327e k__Bacteria; p__Verrucomicrobia; c__[Pedosphaerae]; o__[Pedosphaerales]; f__; g__; s__ 0.999999885192515 -ebcbd71a778e6a1a776d2d50d0801fed k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__ 0.9975013045776004 -c80037fe31359840bb73250f330b60e3 k__Bacteria 0.9727262121442337 -bd759efe26a5b4b869d3fa5e4693080d k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Ruminococcaceae; g__; s__ 0.9995981370005347 -723858f72b4469efb79c323f75bc181f k__Bacteria; p__Planctomycetes; c__Planctomycetia; o__Planctomycetales; f__Planctomycetaceae; g__Planctomyces; s__ 0.9999842079365734 -8021f872c32700d46738f3591cb4c58a k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__; g__; s__ 0.950298422800317 -47c7eb4df73a5d553cd2f7a360ff5872 k__Bacteria 0.9625306758187444 -ad492bcae03f566b36a19e31f04d659a k__Bacteria 0.9592420622809142 -eb8ef4756ed538fe480d979e740a04d8 k__Bacteria 0.9992518268672295 -5db2cf37007f874e25eb2c901917e15a k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__S24-7; g__; s__ 0.9998650088122101 -fa3729663b98de0c0af7913e9f30c19e k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rhodospirillales; f__; g__; s__ 0.7260248247151302 -504572e3afd673db749ee5e8e3e57b97 k__Bacteria; p__Cyanobacteria 0.996420061481882 -a6b6f29a1196cacfc392e3d71f55e2a2 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Bdellovibrionales; f__Bacteriovoracaceae; g__Bacteriovorax; s__ 0.9536660457678927 -0e5df3d01cc073e3c9674c2534169f03 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__[Acidaminobacteraceae]; g__Acidaminobacter; s__ 0.749393658744113 -06845c67bc4203081a981200f33e87eb k__Bacteria; p__Proteobacteria 0.9956180804506998 -98d250a339a635f20e26397dafc6ced3 k__Bacteria; p__Firmicutes; c__Clostridia; o__Clostridiales; f__Clostridiaceae; g__Clostridium; s__ 0.999193575156621 -1830c14ead81ad012f1db0e12f8ab6a4 k__Bacteria; p__TM7; c__TM7-3; o__Blgi18; f__; g__; s__ 0.9226796920359376 diff --git a/q2_composition/_ancombc2_visualizer/tests/featureRecord.test.ts b/q2_composition/_ancombc2_visualizer/tests/featureRecord.test.ts deleted file mode 100644 index 4f7b01e..0000000 --- a/q2_composition/_ancombc2_visualizer/tests/featureRecord.test.ts +++ /dev/null @@ -1,93 +0,0 @@ -import { describe, test, assert } from "vitest"; -import { FeatureRecord, FeatureRecords } from "../src/util/features"; - -describe("FeatureRecord class", () => { - const feature = new FeatureRecord("abc123"); - - feature.addVariable( - feature.createVariable("body-site", "lfc", 2.2, "tongue", "gut"), - ); - feature.addVariable( - feature.createVariable("body-site", "lfc", -0.3, "left palm", "gut"), - ); - feature.addVariable( - feature.createVariable("body-site", "p", 0.05, "left palm", "gut"), - ); - - test("addVariable()", () => { - assert.equal(feature.variables.size, 2); - }); - - test("getVariable()", () => { - let obs = feature.getVariable("body-site", "tongue"); - let exp = { - name: "body-site", - lfc: 2.2, - level: "tongue", - reference: "gut", - }; - assert.deepEqual(obs, exp); - - obs = feature.getVariable("body-site", "left palm"); - exp = { - name: "body-site", - lfc: -0.3, - p: 0.05, - level: "left palm", - reference: "gut", - }; - assert.deepEqual(obs, exp); - }); - - test("getVariableSlice()", () => { - let obs = feature.getVariableSlice("body-site", "lfc", "tongue"); - let exp = 2.2; - assert.equal(obs, exp); - - obs = feature.getVariableSlice("body-site", "p", "left palm"); - exp = 0.05; - assert.equal(obs, exp); - }); -}); - -describe("FeatureRecords class", () => { - const features = new FeatureRecords(); - - const feature1 = new FeatureRecord("abc123"); - feature1.addVariable( - feature1.createVariable("body-site", "lfc", 2.2, "tongue", "gut"), - ); - feature1.addVariable( - feature1.createVariable("body-site", "lfc", -0.3, "left palm", "gut"), - ); - - features.addFeature(feature1); - - test("addFeature()", () => { - assert.equal(features.records.length, 1); - }); - - const feature2 = new FeatureRecord("abc123"); - feature2.addVariable( - feature2.createVariable("body-site", "p", 0.05, "left palm", "gut"), - ); - features.addFeature(feature2); - - test("addFeature() matching feature", () => { - assert.equal(features.records.length, 1); - - assert.equal(features.records[0].variables.size, 2); - }); - - test("addFeature() merges features", () => { - assert.equal(features.records.length, 1); - - const feature = features.getFeature("abc123"); - - const lfc = feature!.getVariableSlice("body-site", "lfc", "left palm"); - assert.equal(lfc, -0.3); - - const p = feature!.getVariableSlice("body-site", "p", "left palm"); - assert.equal(p, 0.05); - }); -}); diff --git a/q2_composition/_ancombc2_visualizer/tests/parse.test.ts b/q2_composition/_ancombc2_visualizer/tests/parse.test.ts deleted file mode 100644 index b1065a7..0000000 --- a/q2_composition/_ancombc2_visualizer/tests/parse.test.ts +++ /dev/null @@ -1,168 +0,0 @@ -import { vi, describe, test, assert } from "vitest"; -import { readFileSync } from "fs"; -import { FeatureRecords } from "../src/util/features"; -import { - getColumnField, - parseJSONLFeatureRecord, - parseSlice, - parseAllSlices, -} from "../src/util/parse"; - -// mock d3.text -async function mockedText(slice: string): Promise { - return readFileSync(slice, "utf-8"); -} -vi.mock("d3-fetch", () => { - return { text: vi.fn(mockedText) }; -}); - -describe("getColumnField()", () => { - const lfcText = readFileSync("tests/data/output-format/lfc.jsonl", "utf-8"); - const header = JSON.parse(lfcText.split("\n")[0]); - - test("column name is present", () => { - const column = "body-site::left palm"; - const exp = { - name: "body-site::left palm", - type: null, - missing: false, - title: "", - description: "", - extra: { - variable: "body-site", - level: "left palm", - reference: "gut", - }, - }; - - assert.deepEqual(getColumnField(column, header), exp); - }); - - test("column name not present", () => { - const column = "waldo"; - - assert.throws( - () => getColumnField(column, header), - "Column waldo not found in JSONL header.", - ); - }); -}); - -describe("parseJSONLFeatureRecord()", () => { - const lfcText = readFileSync("tests/data/output-format/lfc.jsonl", "utf-8"); - const jsonRecords = lfcText - .split("\n") - .filter((line) => line.trim() !== "") - .map((line) => JSON.parse(line)); - - const header = jsonRecords[0]; - const jsonRecord = jsonRecords[1]; - const sliceName = "lfc"; - - const obs = parseJSONLFeatureRecord(jsonRecord, header, sliceName); - - test("parses feature id", () => { - assert.equal(obs.featureId, "4b5eeb300368260019c1fbc7a3c718fc"); - }); - - test("parses correct number of variables", () => { - assert.equal(obs.variables.size, 5); - }); - - test("parses categorical columns", () => { - const variables = Array.from(obs.variables.values()); - const bodySiteVariables = variables.filter( - (v) => v.name == "body-site", - ); - assert.equal(bodySiteVariables.length, 3); - - const levels = bodySiteVariables.map((v) => v.level); - assert.sameMembers(levels, ["right palm", "left palm", "tongue"]); - - const references = bodySiteVariables.map((v) => v.reference); - assert.sameMembers(references, ["gut", "gut", "gut"]); - }); - - test("parses numerical columns", () => { - const variables = Array.from(obs.variables.values()); - const nonCategoricalVariables = variables.filter( - (v) => !Object.hasOwn(v, "reference"), - ); - assert.equal(nonCategoricalVariables.length, 2); - - const yearVariable = nonCategoricalVariables.find( - (v) => v.name == "year", - ); - assert.deepEqual(yearVariable, { - name: "year", - lfc: 189.6871124062, - }); - }); -}); - -describe("parseSlice()", async () => { - const sliceFilepath = "tests/data/output-format/lfc.jsonl"; - const featureRecords = new FeatureRecords(); - await parseSlice(sliceFilepath, featureRecords); - - test("correct number of features", () => { - assert.equal(featureRecords.records.length, 8); - }); - - test("slice parsed correctly", () => { - const feature = featureRecords.getFeature( - "fe30ff0f71a38a39cf1717ec2be3a2fc", - ); - - assert.equal( - feature!.getVariableSlice("body-site", "lfc", "left palm"), - 113.4173262332, - ); - - assert.equal(feature!.getVariableSlice("year", "lfc"), 181.01108921); - - const variable = feature!.getVariable("body-site", "right palm"); - assert.isOk(variable!.lfc); - assert.isNotOk(variable!.q); - assert.isNotOk(variable!.p); - assert.isNotOk(variable!.se); - }); -}); - -describe("parseAllSlices()", async () => { - const sliceDirPath = "tests/data/output-format"; - const featureRecords = new FeatureRecords(); - await parseAllSlices(sliceDirPath, featureRecords); - - test("correct number of features", () => { - assert.equal(featureRecords.records.length, 8); - }); - - test("all slices parsed", () => { - for (let featureRecord of featureRecords.records) { - for (let variable of featureRecord.variables.values()) { - for (let prop of ["lfc", "se", "p", "q"]) { - assert.property(variable, prop); - assert.isDefined(variable[prop]); - } - } - } - }); - - test("structure and contents of arbitrary feature", () => { - const id = "1d2e5f3444ca750c85302ceee2473331"; - const feature = featureRecords.getFeature(id); - - assert.equal( - feature!.getVariableSlice("body-site", "lfc", "left palm"), - 86.9453579935, - ); - - assert.equal(feature!.getVariableSlice("year", "se"), 0.0030650395); - - assert.property( - feature!.getVariable("body-site", "tongue"), - "reference", - ); - }); -}); diff --git a/q2_composition/_ancombc2_visualizer/tests/taxonomy.test.ts b/q2_composition/_ancombc2_visualizer/tests/taxonomy.test.ts deleted file mode 100644 index 7af4b73..0000000 --- a/q2_composition/_ancombc2_visualizer/tests/taxonomy.test.ts +++ /dev/null @@ -1,52 +0,0 @@ -import { vi, describe, test, assert } from "vitest"; -import { readFileSync } from "fs"; -import { TaxonomyNode, parseTaxonomy } from "../src/util/taxonomy"; -import * as d3 from "d3"; - -// mock d3.tsv -async function mockedTsv(slice: string): Promise { - const textData = readFileSync(slice, "utf-8"); - let lines = textData.split("\n").filter((l) => l.trim() != ""); - - // drop header - lines = lines.slice(1); - - let data: object[] = []; - for (let line of lines) { - const values = line.split("\t"); - const record = { - "Feature ID": values[0], - Taxon: values[1], - }; - data.push(record); - } - - return data; -} -vi.mock("d3-fetch", () => { - return { tsv: vi.fn(mockedTsv) }; -}); - -describe("parseTaxonomy()", async () => { - let root: d3.HierarchyNode; - - test("parses successfully", async () => { - root = await parseTaxonomy("tests/data/taxonomy-fake.tsv"); - }); - - test("has correct number of nodes", () => { - assert.equal(root.descendants().length, 12); - }); - - test("root has correct children", () => { - const exp = ["d1", "d2"]; - assert.deepEqual( - root.children!.map((c) => c.data.name), - exp, - ); - }); - - test("back references exist", () => { - assert.equal(root.data.hierarchyNode, root); - }); -}); diff --git a/q2_composition/_ancombc2_visualizer/tsconfig.app.json b/q2_composition/_ancombc2_visualizer/tsconfig.app.json deleted file mode 100644 index 55a2f9b..0000000 --- a/q2_composition/_ancombc2_visualizer/tsconfig.app.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "extends": "@tsconfig/svelte/tsconfig.json", - "compilerOptions": { - "target": "ESNext", - "useDefineForClassFields": true, - "module": "ESNext", - "resolveJsonModule": true, - /** - * Typecheck JS in `.svelte` and `.js` files by default. - * Disable checkJs if you'd like to use dynamic types in JS. - * Note that setting allowJs false does not prevent the use - * of JS in `.svelte` files. - */ - "allowJs": true, - "checkJs": true, - "isolatedModules": true, - "moduleDetection": "force" - }, - "include": ["src/**/*.ts", "src/**/*.js", "src/**/*.svelte"] -} diff --git a/q2_composition/_ancombc2_visualizer/tsconfig.json b/q2_composition/_ancombc2_visualizer/tsconfig.json deleted file mode 100644 index 1ffef60..0000000 --- a/q2_composition/_ancombc2_visualizer/tsconfig.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "files": [], - "references": [ - { "path": "./tsconfig.app.json" }, - { "path": "./tsconfig.node.json" } - ] -} diff --git a/q2_composition/_ancombc2_visualizer/tsconfig.node.json b/q2_composition/_ancombc2_visualizer/tsconfig.node.json deleted file mode 100644 index db0becc..0000000 --- a/q2_composition/_ancombc2_visualizer/tsconfig.node.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "compilerOptions": { - "tsBuildInfoFile": "./node_modules/.tmp/tsconfig.node.tsbuildinfo", - "target": "ES2022", - "lib": ["ES2023"], - "module": "ESNext", - "skipLibCheck": true, - - /* Bundler mode */ - "moduleResolution": "bundler", - "allowImportingTsExtensions": true, - "isolatedModules": true, - "moduleDetection": "force", - "noEmit": true, - - /* Linting */ - "strict": true, - "noUnusedLocals": true, - "noUnusedParameters": true, - "noFallthroughCasesInSwitch": true, - "noUncheckedSideEffectImports": true - }, - "include": ["vite.config.ts"] -} diff --git a/q2_composition/_ancombc2_visualizer/vite.config.ts b/q2_composition/_ancombc2_visualizer/vite.config.ts deleted file mode 100644 index bfeb276..0000000 --- a/q2_composition/_ancombc2_visualizer/vite.config.ts +++ /dev/null @@ -1,9 +0,0 @@ -import { defineConfig } from "vite"; -import { svelte } from "@sveltejs/vite-plugin-svelte"; -import tailwindcss from "@tailwindcss/vite"; - -// https://vite.dev/config/ -export default defineConfig({ - plugins: [svelte(), tailwindcss()], - base: "", -}); From 7557b8d4d2ced4f1d53142a356ad602681b03207 Mon Sep 17 00:00:00 2001 From: Macabe Wood Date: Tue, 26 May 2026 13:54:08 -0700 Subject: [PATCH 07/15] Separating and adding tests --- q2_composition/tests/test_ancombc2.py | 31 +----- .../tests/test_diff_abundance_plot.py | 104 ++++++++++++++++++ 2 files changed, 105 insertions(+), 30 deletions(-) create mode 100644 q2_composition/tests/test_diff_abundance_plot.py diff --git a/q2_composition/tests/test_ancombc2.py b/q2_composition/tests/test_ancombc2.py index c45159d..45a7d9c 100644 --- a/q2_composition/tests/test_ancombc2.py +++ b/q2_composition/tests/test_ancombc2.py @@ -10,7 +10,6 @@ import pandas as pd from pandas.testing import assert_frame_equal -import os from pathlib import Path import subprocess import tempfile @@ -24,7 +23,7 @@ r_base, ancombc2, _process_formula, _convert_metadata, _split_into_slices, _rename_variables_post, _is_categorical, _parse_variable_and_level, _deduce_reference_levels, _process_categorical_variables, - _process_structural_zeros, da_barplot + _process_structural_zeros ) from q2_composition._format import ANCOMBC2SliceMapping @@ -185,34 +184,6 @@ def test_spaces_in_metadata_column(self): # three levels, so one reference and other two in the output self.assertEqual(len(variable_with_spaces_columns), 2) - def test_da_barplot(self): - ''' - Tests that the visualizer runs successfully, which is essentially a - test of whether or not the visualizer got built into the - q2_composition/_da_barplot/dist/ folder successfully. - ''' - with tempfile.TemporaryDirectory() as tempdir: - da_barplot(tempdir, self.abc2_output) - assert os.path.exists(os.path.join(tempdir, 'index.html')) - - def test_da_barplot_non_overlapping_taxonomy(self): - ''' - Tests that an error is raised when attempting to visualize ancombc2 - data with a taxonomy that contains none of the features present in the - ancombc2 data. - ''' - taxonomy_df = pd.DataFrame({ - 'Feature ID': ['feat1', 'feat2'], - 'Taxon': ['taxon1', 'taxon2'], - 'Confidence': [0.9, 0.95] - }) - - with tempfile.TemporaryDirectory() as tempdir: - with self.assertRaisesRegex( - ValueError, 'No features remained in your taxonomy' - ): - da_barplot(tempdir, self.abc2_output, taxonomy_df) - class TestFormulaProcessing(TestANCOMBC2Base): def test_process_formula(self): diff --git a/q2_composition/tests/test_diff_abundance_plot.py b/q2_composition/tests/test_diff_abundance_plot.py new file mode 100644 index 0000000..401936a --- /dev/null +++ b/q2_composition/tests/test_diff_abundance_plot.py @@ -0,0 +1,104 @@ +# ---------------------------------------------------------------------------- +# Copyright (c) 2016-2026, QIIME 2 development team. +# +# Distributed under the terms of the Modified BSD License. +# +# The full license is in the file LICENSE, distributed with this software. +# ---------------------------------------------------------------------------- +import unittest +import qiime2 +import biom +import os +import tempfile +import pandas as pd + +from pathlib import Path +from q2_composition._ancombc2 import da_barplot, ancombc2 +from q2_composition._ancombc import ancombc + + +class TestDiffAbundancePlot(unittest.TestCase): + @classmethod + def setUpClass(cls): + cls.test_data_fp = Path(__file__).parent / 'data' / 'ancombc2' + + table_fp = cls.test_data_fp / 'feature-table.biom' + cls.biom_table = biom.load_table(table_fp) + + metadata_fp = cls.test_data_fp / 'metadata.tsv' + cls.ancombc2_metadata = qiime2.Metadata.load(metadata_fp) + + ancombc_table_fp = Path(__file__).parent / 'data' / 'table-ancombc.qza' + ancombc_table = qiime2.Artifact.load(ancombc_table_fp) + cls.ancombc_table = ancombc_table.view(pd.DataFrame) + + metadata_fp = Path(__file__).parent / 'data' / 'sample-md-ancombc.tsv' + cls.ancombc_metadata = qiime2.Metadata.load(metadata_fp) + + cls.abc2_output = ancombc2( + table=cls.biom_table, + metadata=cls.ancombc2_metadata, + fixed_effects_formula='body-site + year', + group='body-site', + structural_zeros=True + ) + + cls.abc_output = ancombc( + table=cls.ancombc_table, + metadata=cls.ancombc_metadata, + formula='bodysite' + ) + + def test_da_barplot(self): + ''' + Tests that the visualizer runs successfully, which is essentially a + test of whether or not the visualizer got built into the + q2_composition/_da_barplot/dist/ folder successfully. + ''' + with tempfile.TemporaryDirectory() as tempdir: + da_barplot(tempdir, self.abc2_output) + assert os.path.exists(os.path.join(tempdir, 'index.html')) + + with tempfile.TemporaryDirectory() as tempdir: + da_barplot(tempdir, self.abc_output) + assert os.path.exists(os.path.join(tempdir, 'index.html')) + + def test_da_barplot_non_overlapping_taxonomy(self): + ''' + Tests that an error is raised when attempting to visualize ancombc2 + data with a taxonomy that contains none of the features present in the + ancombc2 data. + ''' + taxonomy_df = pd.DataFrame({ + 'Feature ID': ['feat1', 'feat2'], + 'Taxon': ['taxon1', 'taxon2'], + 'Confidence': [0.9, 0.95] + }) + + with tempfile.TemporaryDirectory() as tempdir: + with self.assertRaisesRegex( + ValueError, 'No features remained in your taxonomy' + ): + da_barplot(tempdir, self.abc2_output, taxonomy_df) + + with tempfile.TemporaryDirectory() as tempdir: + with self.assertRaisesRegex( + ValueError, 'No features remained in your taxonomy' + ): + da_barplot(tempdir, self.abc_output, taxonomy_df) + + def test_da_barplot_accepts_ancombc2(self): + ''' + Tests that da_barplot accepts ancombc2 outputs. + ''' + with tempfile.TemporaryDirectory() as tempdir: + da_barplot(tempdir, self.abc2_output) + assert os.path.exists(os.path.join(tempdir, 'index.html')) + + def test_da_barplot_accepts_ancombc(self): + ''' + Tests that da_barplot accepts ancombc outputs. + ''' + with tempfile.TemporaryDirectory() as tempdir: + da_barplot(tempdir, self.abc_output) + assert os.path.exists(os.path.join(tempdir, 'index.html')) From 18d236a645f408cadda1743157271ead4ae155eb Mon Sep 17 00:00:00 2001 From: Macabe Wood Date: Wed, 3 Jun 2026 10:30:15 -0700 Subject: [PATCH 08/15] tests for da_barplot action --- .../tests/test_diff_abundance_plot.py | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/q2_composition/tests/test_diff_abundance_plot.py b/q2_composition/tests/test_diff_abundance_plot.py index 401936a..87afeea 100644 --- a/q2_composition/tests/test_diff_abundance_plot.py +++ b/q2_composition/tests/test_diff_abundance_plot.py @@ -15,6 +15,8 @@ from pathlib import Path from q2_composition._ancombc2 import da_barplot, ancombc2 from q2_composition._ancombc import ancombc +from qiime2.sdk import PluginManager +from qiime2 import Artifact class TestDiffAbundancePlot(unittest.TestCase): @@ -102,3 +104,33 @@ def test_da_barplot_accepts_ancombc(self): with tempfile.TemporaryDirectory() as tempdir: da_barplot(tempdir, self.abc_output) assert os.path.exists(os.path.join(tempdir, 'index.html')) + + def test_da_barplot_action_ancombc2(self): + pm = PluginManager() + da_barplot = pm.plugins['composition'].actions['da_barplot'] + + ancombc2_artifact = Artifact.import_data( + type='FeatureData[ANCOMBC2Output]', view=self.abc2_output + ) + + viz = da_barplot(ancombc2_artifact) + viz = viz.visualization + + with tempfile.TemporaryDirectory() as tempdir: + viz.export_data(tempdir) + assert os.path.exists(os.path.join(tempdir, 'index.html')) + + def test_da_barplot_action_ancombc(self): + pm = PluginManager() + da_barplot = pm.plugins['composition'].actions['da_barplot'] + + ancombc_artifact = Artifact.import_data( + type='FeatureData[DifferentialAbundance]', view=self.abc_output + ) + + viz = da_barplot(ancombc_artifact) + viz = viz.visualization + + with tempfile.TemporaryDirectory() as tempdir: + viz.export_data(tempdir) + assert os.path.exists(os.path.join(tempdir, 'index.html')) From 03140122883a6cd0a697ea759e99815bf1b75664 Mon Sep 17 00:00:00 2001 From: Macabe Wood Date: Wed, 3 Jun 2026 12:26:00 -0700 Subject: [PATCH 09/15] github test From 7296973ae606b3cf28ed36e0ce2b8e61a856dc6e Mon Sep 17 00:00:00 2001 From: Oddant1 Date: Wed, 24 Jun 2026 11:31:52 -0700 Subject: [PATCH 10/15] Have ancombc2 return ANCOMBC2SliceMapping --- q2_composition/_ancombc2.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/q2_composition/_ancombc2.py b/q2_composition/_ancombc2.py index 5e2978d..ac25bac 100644 --- a/q2_composition/_ancombc2.py +++ b/q2_composition/_ancombc2.py @@ -54,7 +54,7 @@ def ancombc2( alpha: float = 0.05, diff_robust: bool = False, num_processes: int = 1, -) -> ANCOMBC2OutputDirFmt: +) -> ANCOMBC2SliceMapping: ''' Wraps the `ancombc2` R function from the ANCOMBC package. @@ -64,10 +64,8 @@ def ancombc2( Returns ------- - ANCOMBC2OutputDirFmt - A directory format containing the ANCOMBC2 model's per-feature - statistics and per-feature structural zero designations if - `structural_zeros` is set. + ANCOMBC2SliceMapping + A dictionary mapping the name of the slice to the slice's columns. ''' if structural_zeros and group is None: msg = ( @@ -114,6 +112,8 @@ def ancombc2( model_statistics_df = ro.conversion.get_conversion().rpy2py( model_statistics ) + model_statistics_df['taxon'] = \ + model_statistics_df['taxon'].astype('string') slices = _split_into_slices(model_statistics_df, diff_robust) @@ -133,7 +133,7 @@ def ancombc2( # split categorical variables from levels and annotate references slices = _process_categorical_variables(slices, metadata, table) - return transform(data=slices, to_type=ANCOMBC2OutputDirFmt) + return slices def _process_formula(formula: str, metadata: qiime2.Metadata) -> str: From f5bb50d1c10ea33acd9af0a80193847b1c3af537 Mon Sep 17 00:00:00 2001 From: Oddant1 Date: Wed, 24 Jun 2026 11:31:58 -0700 Subject: [PATCH 11/15] Update tests --- q2_composition/tests/test_ancombc2.py | 15 ++++++--------- q2_composition/tests/test_diff_abundance_plot.py | 13 ++++++++++--- 2 files changed, 16 insertions(+), 12 deletions(-) diff --git a/q2_composition/tests/test_ancombc2.py b/q2_composition/tests/test_ancombc2.py index 45a7d9c..241a37b 100644 --- a/q2_composition/tests/test_ancombc2.py +++ b/q2_composition/tests/test_ancombc2.py @@ -25,7 +25,7 @@ _deduce_reference_levels, _process_categorical_variables, _process_structural_zeros ) -from q2_composition._format import ANCOMBC2SliceMapping +from q2_composition._format import ANCOMBC2SliceMapping, ANCOMBC2OutputDirFmt class TestANCOMBC2Base(unittest.TestCase): @@ -119,7 +119,7 @@ def test_wrapped_ancombc2(self): 'q2_composition._ancombc2._process_structural_zeros', side_effect=lambda structural_zeros: structural_zeros ): - output_format = ancombc2( + slices = ancombc2( table=self.biom_table, metadata=self.metadata, fixed_effects_formula='body-site + year', @@ -128,11 +128,11 @@ def test_wrapped_ancombc2(self): diff_robust=True, ) - slices = transform(data=output_format, to_type=ANCOMBC2SliceMapping) + output_format = transform(data=slices, to_type=ANCOMBC2OutputDirFmt) model_stats = self._slices_to_single_df(slices) struc_zeros = output_format.structural_zeros.view(pd.DataFrame) - + assert_frame_equal( ground_truth_model_stats, model_stats, check_like=True ) @@ -145,8 +145,7 @@ def test_ancombc2_without_diff_robust(self): Ensure that the `diff_robust` slice is not present by default in the output format. ''' - slices = transform(data=self.abc2_output, to_type=ANCOMBC2SliceMapping) - self.assertNotIn('diff_robust', slices) + self.assertNotIn('diff_robust', self.abc2_output) def test_group_enforced_if_structural_zeros(self): ''' @@ -168,14 +167,12 @@ def test_spaces_in_metadata_column(self): ''' Tests that metadata columns that contain spaces are handled properly. ''' - output_format = ancombc2( + slices = ancombc2( table=self.biom_table, metadata=self.metadata, fixed_effects_formula='Variable with spaces', ) - slices = transform(data=output_format, to_type=ANCOMBC2SliceMapping) - lfc_slice_columns = list(slices['lfc'].columns) variable_with_spaces_columns = [ col for col in lfc_slice_columns if 'Variable with spaces::' in col diff --git a/q2_composition/tests/test_diff_abundance_plot.py b/q2_composition/tests/test_diff_abundance_plot.py index 87afeea..d814e98 100644 --- a/q2_composition/tests/test_diff_abundance_plot.py +++ b/q2_composition/tests/test_diff_abundance_plot.py @@ -15,6 +15,7 @@ from pathlib import Path from q2_composition._ancombc2 import da_barplot, ancombc2 from q2_composition._ancombc import ancombc +from q2_composition._format import ANCOMBC2OutputDirFmt from qiime2.sdk import PluginManager from qiime2 import Artifact @@ -45,6 +46,12 @@ def setUpClass(cls): structural_zeros=True ) + # Use this for raw calls to da_barplot but use the original for when we + # load it to an Artifact and invoke the action + cls.abc2_output_DirFmt = qiime2.plugin.util.transform( + data=cls.abc2_output, to_type=ANCOMBC2OutputDirFmt + ) + cls.abc_output = ancombc( table=cls.ancombc_table, metadata=cls.ancombc_metadata, @@ -58,7 +65,7 @@ def test_da_barplot(self): q2_composition/_da_barplot/dist/ folder successfully. ''' with tempfile.TemporaryDirectory() as tempdir: - da_barplot(tempdir, self.abc2_output) + da_barplot(tempdir, self.abc2_output_DirFmt) assert os.path.exists(os.path.join(tempdir, 'index.html')) with tempfile.TemporaryDirectory() as tempdir: @@ -81,7 +88,7 @@ def test_da_barplot_non_overlapping_taxonomy(self): with self.assertRaisesRegex( ValueError, 'No features remained in your taxonomy' ): - da_barplot(tempdir, self.abc2_output, taxonomy_df) + da_barplot(tempdir, self.abc2_output_DirFmt, taxonomy_df) with tempfile.TemporaryDirectory() as tempdir: with self.assertRaisesRegex( @@ -94,7 +101,7 @@ def test_da_barplot_accepts_ancombc2(self): Tests that da_barplot accepts ancombc2 outputs. ''' with tempfile.TemporaryDirectory() as tempdir: - da_barplot(tempdir, self.abc2_output) + da_barplot(tempdir, self.abc2_output_DirFmt) assert os.path.exists(os.path.join(tempdir, 'index.html')) def test_da_barplot_accepts_ancombc(self): From 909f7f2e142ed19313c021193e3b6c5c350bfb74 Mon Sep 17 00:00:00 2001 From: Oddant1 Date: Wed, 24 Jun 2026 11:32:19 -0700 Subject: [PATCH 12/15] whitespace --- q2_composition/tests/test_ancombc2.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/q2_composition/tests/test_ancombc2.py b/q2_composition/tests/test_ancombc2.py index 241a37b..b957b24 100644 --- a/q2_composition/tests/test_ancombc2.py +++ b/q2_composition/tests/test_ancombc2.py @@ -132,7 +132,7 @@ def test_wrapped_ancombc2(self): model_stats = self._slices_to_single_df(slices) struc_zeros = output_format.structural_zeros.view(pd.DataFrame) - + assert_frame_equal( ground_truth_model_stats, model_stats, check_like=True ) From d7c81ef8e7d902cc85ebd3873bf1ab5706cd4376 Mon Sep 17 00:00:00 2001 From: Macabe Wood Date: Wed, 24 Jun 2026 14:09:58 -0700 Subject: [PATCH 13/15] Revert "Ancombc2 refactor" --- q2_composition/_ancombc2.py | 12 ++++++------ q2_composition/tests/test_ancombc2.py | 13 ++++++++----- q2_composition/tests/test_diff_abundance_plot.py | 13 +++---------- 3 files changed, 17 insertions(+), 21 deletions(-) diff --git a/q2_composition/_ancombc2.py b/q2_composition/_ancombc2.py index ac25bac..5e2978d 100644 --- a/q2_composition/_ancombc2.py +++ b/q2_composition/_ancombc2.py @@ -54,7 +54,7 @@ def ancombc2( alpha: float = 0.05, diff_robust: bool = False, num_processes: int = 1, -) -> ANCOMBC2SliceMapping: +) -> ANCOMBC2OutputDirFmt: ''' Wraps the `ancombc2` R function from the ANCOMBC package. @@ -64,8 +64,10 @@ def ancombc2( Returns ------- - ANCOMBC2SliceMapping - A dictionary mapping the name of the slice to the slice's columns. + ANCOMBC2OutputDirFmt + A directory format containing the ANCOMBC2 model's per-feature + statistics and per-feature structural zero designations if + `structural_zeros` is set. ''' if structural_zeros and group is None: msg = ( @@ -112,8 +114,6 @@ def ancombc2( model_statistics_df = ro.conversion.get_conversion().rpy2py( model_statistics ) - model_statistics_df['taxon'] = \ - model_statistics_df['taxon'].astype('string') slices = _split_into_slices(model_statistics_df, diff_robust) @@ -133,7 +133,7 @@ def ancombc2( # split categorical variables from levels and annotate references slices = _process_categorical_variables(slices, metadata, table) - return slices + return transform(data=slices, to_type=ANCOMBC2OutputDirFmt) def _process_formula(formula: str, metadata: qiime2.Metadata) -> str: diff --git a/q2_composition/tests/test_ancombc2.py b/q2_composition/tests/test_ancombc2.py index b957b24..45a7d9c 100644 --- a/q2_composition/tests/test_ancombc2.py +++ b/q2_composition/tests/test_ancombc2.py @@ -25,7 +25,7 @@ _deduce_reference_levels, _process_categorical_variables, _process_structural_zeros ) -from q2_composition._format import ANCOMBC2SliceMapping, ANCOMBC2OutputDirFmt +from q2_composition._format import ANCOMBC2SliceMapping class TestANCOMBC2Base(unittest.TestCase): @@ -119,7 +119,7 @@ def test_wrapped_ancombc2(self): 'q2_composition._ancombc2._process_structural_zeros', side_effect=lambda structural_zeros: structural_zeros ): - slices = ancombc2( + output_format = ancombc2( table=self.biom_table, metadata=self.metadata, fixed_effects_formula='body-site + year', @@ -128,7 +128,7 @@ def test_wrapped_ancombc2(self): diff_robust=True, ) - output_format = transform(data=slices, to_type=ANCOMBC2OutputDirFmt) + slices = transform(data=output_format, to_type=ANCOMBC2SliceMapping) model_stats = self._slices_to_single_df(slices) struc_zeros = output_format.structural_zeros.view(pd.DataFrame) @@ -145,7 +145,8 @@ def test_ancombc2_without_diff_robust(self): Ensure that the `diff_robust` slice is not present by default in the output format. ''' - self.assertNotIn('diff_robust', self.abc2_output) + slices = transform(data=self.abc2_output, to_type=ANCOMBC2SliceMapping) + self.assertNotIn('diff_robust', slices) def test_group_enforced_if_structural_zeros(self): ''' @@ -167,12 +168,14 @@ def test_spaces_in_metadata_column(self): ''' Tests that metadata columns that contain spaces are handled properly. ''' - slices = ancombc2( + output_format = ancombc2( table=self.biom_table, metadata=self.metadata, fixed_effects_formula='Variable with spaces', ) + slices = transform(data=output_format, to_type=ANCOMBC2SliceMapping) + lfc_slice_columns = list(slices['lfc'].columns) variable_with_spaces_columns = [ col for col in lfc_slice_columns if 'Variable with spaces::' in col diff --git a/q2_composition/tests/test_diff_abundance_plot.py b/q2_composition/tests/test_diff_abundance_plot.py index d814e98..87afeea 100644 --- a/q2_composition/tests/test_diff_abundance_plot.py +++ b/q2_composition/tests/test_diff_abundance_plot.py @@ -15,7 +15,6 @@ from pathlib import Path from q2_composition._ancombc2 import da_barplot, ancombc2 from q2_composition._ancombc import ancombc -from q2_composition._format import ANCOMBC2OutputDirFmt from qiime2.sdk import PluginManager from qiime2 import Artifact @@ -46,12 +45,6 @@ def setUpClass(cls): structural_zeros=True ) - # Use this for raw calls to da_barplot but use the original for when we - # load it to an Artifact and invoke the action - cls.abc2_output_DirFmt = qiime2.plugin.util.transform( - data=cls.abc2_output, to_type=ANCOMBC2OutputDirFmt - ) - cls.abc_output = ancombc( table=cls.ancombc_table, metadata=cls.ancombc_metadata, @@ -65,7 +58,7 @@ def test_da_barplot(self): q2_composition/_da_barplot/dist/ folder successfully. ''' with tempfile.TemporaryDirectory() as tempdir: - da_barplot(tempdir, self.abc2_output_DirFmt) + da_barplot(tempdir, self.abc2_output) assert os.path.exists(os.path.join(tempdir, 'index.html')) with tempfile.TemporaryDirectory() as tempdir: @@ -88,7 +81,7 @@ def test_da_barplot_non_overlapping_taxonomy(self): with self.assertRaisesRegex( ValueError, 'No features remained in your taxonomy' ): - da_barplot(tempdir, self.abc2_output_DirFmt, taxonomy_df) + da_barplot(tempdir, self.abc2_output, taxonomy_df) with tempfile.TemporaryDirectory() as tempdir: with self.assertRaisesRegex( @@ -101,7 +94,7 @@ def test_da_barplot_accepts_ancombc2(self): Tests that da_barplot accepts ancombc2 outputs. ''' with tempfile.TemporaryDirectory() as tempdir: - da_barplot(tempdir, self.abc2_output_DirFmt) + da_barplot(tempdir, self.abc2_output) assert os.path.exists(os.path.join(tempdir, 'index.html')) def test_da_barplot_accepts_ancombc(self): From db9c109ba59a449a76c32dcaeb8bcb4e061906c4 Mon Sep 17 00:00:00 2001 From: Oddant1 Date: Thu, 25 Jun 2026 12:29:23 -0700 Subject: [PATCH 14/15] Reapply "Ancombc2 refactor" This reverts commit d7c81ef8e7d902cc85ebd3873bf1ab5706cd4376. --- q2_composition/_ancombc2.py | 12 ++++++------ q2_composition/tests/test_ancombc2.py | 13 +++++-------- q2_composition/tests/test_diff_abundance_plot.py | 13 ++++++++++--- 3 files changed, 21 insertions(+), 17 deletions(-) diff --git a/q2_composition/_ancombc2.py b/q2_composition/_ancombc2.py index 5e2978d..ac25bac 100644 --- a/q2_composition/_ancombc2.py +++ b/q2_composition/_ancombc2.py @@ -54,7 +54,7 @@ def ancombc2( alpha: float = 0.05, diff_robust: bool = False, num_processes: int = 1, -) -> ANCOMBC2OutputDirFmt: +) -> ANCOMBC2SliceMapping: ''' Wraps the `ancombc2` R function from the ANCOMBC package. @@ -64,10 +64,8 @@ def ancombc2( Returns ------- - ANCOMBC2OutputDirFmt - A directory format containing the ANCOMBC2 model's per-feature - statistics and per-feature structural zero designations if - `structural_zeros` is set. + ANCOMBC2SliceMapping + A dictionary mapping the name of the slice to the slice's columns. ''' if structural_zeros and group is None: msg = ( @@ -114,6 +112,8 @@ def ancombc2( model_statistics_df = ro.conversion.get_conversion().rpy2py( model_statistics ) + model_statistics_df['taxon'] = \ + model_statistics_df['taxon'].astype('string') slices = _split_into_slices(model_statistics_df, diff_robust) @@ -133,7 +133,7 @@ def ancombc2( # split categorical variables from levels and annotate references slices = _process_categorical_variables(slices, metadata, table) - return transform(data=slices, to_type=ANCOMBC2OutputDirFmt) + return slices def _process_formula(formula: str, metadata: qiime2.Metadata) -> str: diff --git a/q2_composition/tests/test_ancombc2.py b/q2_composition/tests/test_ancombc2.py index 45a7d9c..b957b24 100644 --- a/q2_composition/tests/test_ancombc2.py +++ b/q2_composition/tests/test_ancombc2.py @@ -25,7 +25,7 @@ _deduce_reference_levels, _process_categorical_variables, _process_structural_zeros ) -from q2_composition._format import ANCOMBC2SliceMapping +from q2_composition._format import ANCOMBC2SliceMapping, ANCOMBC2OutputDirFmt class TestANCOMBC2Base(unittest.TestCase): @@ -119,7 +119,7 @@ def test_wrapped_ancombc2(self): 'q2_composition._ancombc2._process_structural_zeros', side_effect=lambda structural_zeros: structural_zeros ): - output_format = ancombc2( + slices = ancombc2( table=self.biom_table, metadata=self.metadata, fixed_effects_formula='body-site + year', @@ -128,7 +128,7 @@ def test_wrapped_ancombc2(self): diff_robust=True, ) - slices = transform(data=output_format, to_type=ANCOMBC2SliceMapping) + output_format = transform(data=slices, to_type=ANCOMBC2OutputDirFmt) model_stats = self._slices_to_single_df(slices) struc_zeros = output_format.structural_zeros.view(pd.DataFrame) @@ -145,8 +145,7 @@ def test_ancombc2_without_diff_robust(self): Ensure that the `diff_robust` slice is not present by default in the output format. ''' - slices = transform(data=self.abc2_output, to_type=ANCOMBC2SliceMapping) - self.assertNotIn('diff_robust', slices) + self.assertNotIn('diff_robust', self.abc2_output) def test_group_enforced_if_structural_zeros(self): ''' @@ -168,14 +167,12 @@ def test_spaces_in_metadata_column(self): ''' Tests that metadata columns that contain spaces are handled properly. ''' - output_format = ancombc2( + slices = ancombc2( table=self.biom_table, metadata=self.metadata, fixed_effects_formula='Variable with spaces', ) - slices = transform(data=output_format, to_type=ANCOMBC2SliceMapping) - lfc_slice_columns = list(slices['lfc'].columns) variable_with_spaces_columns = [ col for col in lfc_slice_columns if 'Variable with spaces::' in col diff --git a/q2_composition/tests/test_diff_abundance_plot.py b/q2_composition/tests/test_diff_abundance_plot.py index 87afeea..d814e98 100644 --- a/q2_composition/tests/test_diff_abundance_plot.py +++ b/q2_composition/tests/test_diff_abundance_plot.py @@ -15,6 +15,7 @@ from pathlib import Path from q2_composition._ancombc2 import da_barplot, ancombc2 from q2_composition._ancombc import ancombc +from q2_composition._format import ANCOMBC2OutputDirFmt from qiime2.sdk import PluginManager from qiime2 import Artifact @@ -45,6 +46,12 @@ def setUpClass(cls): structural_zeros=True ) + # Use this for raw calls to da_barplot but use the original for when we + # load it to an Artifact and invoke the action + cls.abc2_output_DirFmt = qiime2.plugin.util.transform( + data=cls.abc2_output, to_type=ANCOMBC2OutputDirFmt + ) + cls.abc_output = ancombc( table=cls.ancombc_table, metadata=cls.ancombc_metadata, @@ -58,7 +65,7 @@ def test_da_barplot(self): q2_composition/_da_barplot/dist/ folder successfully. ''' with tempfile.TemporaryDirectory() as tempdir: - da_barplot(tempdir, self.abc2_output) + da_barplot(tempdir, self.abc2_output_DirFmt) assert os.path.exists(os.path.join(tempdir, 'index.html')) with tempfile.TemporaryDirectory() as tempdir: @@ -81,7 +88,7 @@ def test_da_barplot_non_overlapping_taxonomy(self): with self.assertRaisesRegex( ValueError, 'No features remained in your taxonomy' ): - da_barplot(tempdir, self.abc2_output, taxonomy_df) + da_barplot(tempdir, self.abc2_output_DirFmt, taxonomy_df) with tempfile.TemporaryDirectory() as tempdir: with self.assertRaisesRegex( @@ -94,7 +101,7 @@ def test_da_barplot_accepts_ancombc2(self): Tests that da_barplot accepts ancombc2 outputs. ''' with tempfile.TemporaryDirectory() as tempdir: - da_barplot(tempdir, self.abc2_output) + da_barplot(tempdir, self.abc2_output_DirFmt) assert os.path.exists(os.path.join(tempdir, 'index.html')) def test_da_barplot_accepts_ancombc(self): From bba7aa92d94da26decb9c6f40962775e10601919 Mon Sep 17 00:00:00 2001 From: Colin Wood Date: Tue, 7 Jul 2026 11:59:29 -0700 Subject: [PATCH 15/15] small --- q2_composition/_ancombc2.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/q2_composition/_ancombc2.py b/q2_composition/_ancombc2.py index ac25bac..7639297 100644 --- a/q2_composition/_ancombc2.py +++ b/q2_composition/_ancombc2.py @@ -26,11 +26,8 @@ import qiime2 from qiime2.metadata import NumericMetadataColumn, CategoricalMetadataColumn from qiime2.plugin.util import transform -from typing import Union -from q2_composition._format import ( - ANCOMBC2OutputDirFmt, ANCOMBC2SliceMapping, DataLoafPackageDirFmt -) +from q2_composition._format import ANCOMBC2OutputDirFmt, ANCOMBC2SliceMapping r_base = importr('base') r_stats = importr('stats') @@ -856,7 +853,7 @@ def _rename(column: str) -> str: def da_barplot( output_dir: str, - data: Union[ANCOMBC2OutputDirFmt, DataLoafPackageDirFmt], + data: ANCOMBC2OutputDirFmt, taxonomy: pd.DataFrame = None ): ''' @@ -868,7 +865,7 @@ def da_barplot( ---------- output_dir : str The path to the data/ directory in the to-be-created visualization. - data : ANCOMBC2SliceMapping + data : ANCOMBC2OutputDirFmt The ancombc2 slice data to visualize taxonomy : pd.DataFrame | None The taxonomy associated with the features present in `slices`.