page_data_summary.md

Brieflow Visualization App - Page Data Summary

This document provides a summary of the pages in the Brieflow Visualization application, including the data files used and fields accessed by each page.

Pages Overview

Home.py

Data Files Used:

• ../README.md

Fields Used:

• Text content

1_Quality_Control.py

Data Files Used:

• PNG and TSV files from analysis_root
• Files filtered by: 'phenotype', 'merge', 'sbs', 'aggregate' and 'eval'

Fields Used:

• dir_level_0 (Phase): Extracted from the first level of the directory path by splitting the path and indexing
• dir_level_2 (Subgroup): Extracted from the third level of the directory path by splitting the path and indexing
• plate_id: Extracted using regex pattern r'(P-\d+)' to find plate IDs in format "P-123" from the file path
• well_id: Extracted using regex pattern r'(W-[A-Z]\d+)' to find well IDs in format "W-A1", "W-B12", etc. from the file path
• metric_name: Extracted from the file basename by splitting on "__" and taking the last part (e.g., "image__metric_name.png")
• file_path: Stores the relative path of the file from the root directory

2_Cluster.py

Data Files Used:

• TSV files: *__phate_leiden_uniprot.tsv
• PNG and TSV files from 'cluster/plots'

Fields Used:

• PHATE_0, PHATE_1 (coordinates)
• gene_symbol_0
• cluster
• Gene Names
• source
• dir_level_0, dir_level_1
• metric_name

3_Config.py

Data Files Used:

• Git repository information
• requirements.in
• requirements.txt

Fields Used:

• Repository URL
• Commit hash
• Package dependencies

4_Montages.py

Data Files Used:

• PNG files from 'montages' directory

Fields Used:

• gene (extracted from file path directory structure)
• guide (extracted from file path directory structure)
• channel (extracted from file path directory structure)
• file_path

These fields are extracted from the directory structure of the file paths. For example:

Real path example: analysis_root/montages/BRCA1/sgRNA_1234/GFP__cell_image.png

The same path with placeholder variables: analysis_root/montages/{gene}/{guide}/{channel}__filename.png

Where:

• gene = "BRCA1" (third-to-last directory component)
• guide = "sgRNA_1234" (second-to-last directory component)
• channel = "GFP" (first part of the filename before "__")