From 4701f4d155bf463da4f63642f5ae466ac51a7667 Mon Sep 17 00:00:00 2001 From: OJWatson Date: Fri, 25 May 2018 10:16:31 +0100 Subject: [PATCH 1/3] mipmapper_file test and pkgdown refernece updates/. --- R/misc.R | 7 ++++--- docs/reference/mipmapper_file.html | 3 +-- docs/reference/plot_coverage-1.png | Bin 67238 -> 11013 bytes man/mipmapper_file.Rd | 2 +- tests/testthat/Rplots.pdf | Bin 4913 -> 0 bytes tests/testthat/test-misc.R | 6 ++++++ 6 files changed, 12 insertions(+), 6 deletions(-) delete mode 100644 tests/testthat/Rplots.pdf diff --git a/R/misc.R b/R/misc.R index bdfe9a4..46c9fa2 100644 --- a/R/misc.R +++ b/R/misc.R @@ -29,7 +29,7 @@ is.int_vector <- function(x) { x == as.integer(x) } -# load system file --------------------------------------------------------------- +# load system file ------------------------------------------------------------ #' @title Load system file #' #' @description Load system file @@ -40,10 +40,11 @@ is.int_vector <- function(x) { #' #' @export #' @examples -#' # TODO +#' dat <- mipmapper_file("dummy_data.csv") mipmapper_file <- function(name) { - name_full <- system.file("extdata/", name, package='mipmapper', mustWork = TRUE) + name_full <- system.file("extdata/", name, package='mipmapper', + mustWork = TRUE) ret <- fast_read(name_full) return(ret) diff --git a/docs/reference/mipmapper_file.html b/docs/reference/mipmapper_file.html index 77cb2bc..bb72205 100644 --- a/docs/reference/mipmapper_file.html +++ b/docs/reference/mipmapper_file.html @@ -117,8 +117,7 @@

Details

Examples

- 
# TODO
-
+ 
dat <- mipmapper_file("dummy_data.csv")
diff --git a/docs/index.html b/docs/index.html index 81e0890..3baaac1 100644 --- a/docs/index.html +++ b/docs/index.html @@ -74,7 +74,7 @@

In R, ensure that you have the devtools package installed by running

install.packages("devtools", repos='http://cran.us.r-project.org')

Then we can simply install the mipmapper package directly from GitHub by running

-
devtools::install_github("mrc-ide/mipmapper")
+
devtools::install_github("mrc-ide/mipmapper")

And we can load the package by running

library(mipmapper)
@@ -86,12 +86,12 @@

# dat0 <- fast_read("path_to_your_data/NeutralSNPs_AheroYombo.csv") # here we will use in-built example data -dat0 <- mipmapper_file("dummy_data.csv") +dat0 <- mipmapper_file("dummy_data.csv")

Some miscellaneous filtering. Subset to SNPs only (i.e. no more complex mutations), group all alternative alleles together as a single “non-reference” allele, and drop irregular loci (for example non-integer barcode counts).

dat1 <- filter_misc(dat0, SNP_only = TRUE, group_Alt = TRUE, drop_irregular = TRUE)

Next we want to filter based on coverage, throwing away any loci that are below a minimum coverage level. We can visualise how much data will be left at different thresholds using the following function:

plot_coverage(dat1)
-

+

Choose a threshold that strikes a balance between data quantity and quality. Once you have chosen a threshold, apply the filtering as follows:

my_threshold <- 6
 dat3 <- filter_coverage(dat1, min_coverage = my_threshold)
@@ -108,17 +108,17 @@

We can view the variance explained by each compenet graphically using:

plot_pca_variance(pca)
- +

And lastly we can plot the actual prinical component analysis, to see how it has clustered our data:

plot_pca(pca, num_components = 2, meta_var = "Country")
- +

We can control whether we want to visualise the first 2 or 3 components, with the num_componenets argument:

plot_pca(pca, num_components = 3, meta_var = "Country")
- +
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15:43:48 +0100 Subject: [PATCH 3/3] pkgdown fix --- README.Rmd | 1 - README.md | 6 ------ pkgdown_link_formats.R | 1 + 3 files changed, 1 insertion(+), 7 deletions(-) diff --git a/README.Rmd b/README.Rmd index f527ac9..ac4c8a5 100644 --- a/README.Rmd +++ b/README.Rmd @@ -1,6 +1,5 @@ --- output: github_document -always_allow_html: yes --- ```{r, echo = FALSE} knitr::opts_chunk$set( diff --git a/README.md b/README.md index dbe3927..6fdada4 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,3 @@ ---- -output: github_document -always_allow_html: yes ---- - - # mipmapper [![Travis build status](https://travis-ci.org/mrc-ide/mipmapper.svg?branch=master)](https://travis-ci.org/mrc-ide/mipmapper) [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/mrc-ide/mipmapper?branch=master&svg=true)](https://ci.appveyor.com/project/mrc-ide/mipmapper) diff --git a/pkgdown_link_formats.R b/pkgdown_link_formats.R index b4e2483..06325cf 100644 --- a/pkgdown_link_formats.R +++ b/pkgdown_link_formats.R @@ -8,6 +8,7 @@ pkgdown::build_site() # change lines in README.md to make link point to tools lines <- readLines("README.md") +lines <- lines[-c(1:(which(grepl("# mipmapper",lines))-1))] lines[grep("(.*png)",lines)] <- gsub("!\\[\\]\\(R","!\\[\\](tools/R",lines[grep("(.*png)",lines)]) writeLines(lines, "README.md")