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Sfitz fix plot venn bug #232

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merged 5 commits into from
Sep 28, 2023
Merged

Sfitz fix plot venn bug #232

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5d1b6dc
updated plot-venn.R
sorelfitzgibbon Sep 20, 2023
175fe6e
update changelog
sorelfitzgibbon Sep 20, 2023
e409761
fix lintr
sorelfitzgibbon Sep 20, 2023
c00375b
column number variable added
sorelfitzgibbon Sep 22, 2023
665201f
Merge branch 'main' of github.com:uclahs-cds/pipeline-call-sSNV into …
sorelfitzgibbon Sep 27, 2023
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -15,6 +15,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [7.0.0-rc.1] - 2023-08-28

### Changed
- Update plot-venn.R to work with all numbers of algorithms greater than two

### Added
- Add compression of `SomaticSniper` `bam-readcount` output and move to `intermediate` directory
- Add `ncbi_build` parameter
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30 changes: 19 additions & 11 deletions r-scripts/plot-venn.R
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Expand Up @@ -18,12 +18,20 @@ parser$add_argument('-s', '--isec_sites', help = 'The sites.txt file from BCFtoo
parser$add_argument('-o', '--outfile', help = 'Output filename', type = 'character');
args <- parser$parse_args();

## config ##########################################################################################
color.map <- list(
Mutect2 = 'orange',
SomaticSniper = 'red',
MuSE = 'green',
Strelka2 = 'blue'
)

## Function: plot venn diagram #####################################################################
plot.venn <- function(tool.variants, outfile) {
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@sorelfitzgibbon
I have adapted your script for plotting and changed some settings of venn.diagram here: https://github.com/uclahs-cds/project-disease-HeadNeckTumor-ATHC-000072-WholeGenomeLandscape/blob/b1c5fe1d7244aeea37ca40bcb4b2b8bd948b3057/analysis_WGS/pipeline/recSNV/consensusVCF/plot.venn.diagram.R#L41

You can check if some of the arguments might be useful to you?

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Worth looking into if any arguments can be used/added

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@maotian06 and I decided nothing needs to be added at this time

VennDiagram::venn.diagram(
tool.variants.ordered,
tool.variants,
filename = outfile,
fill = c('orange', 'red', 'green', 'blue'),
fill = unlist(color.map[algorithms]),
lty = 'dashed',
cex = 1,
cat.cex = 0.8,
Expand All @@ -39,18 +47,18 @@ algorithms <- gsub('isec-1-or-more.*\t', '', algorithms);
algorithms <- gsub('-.*', '', algorithms);

sites <- read.table(args$isec_sites, header = FALSE, colClasses = 'character');
sites.original.ncol <- ncol(sites);
split.col <- strsplit(as.character(sites$V5), '');
sites$col1 <- sapply(split.col, '[', 1);
sites$col2 <- sapply(split.col, '[', 2);
sites$col3 <- sapply(split.col, '[', 3);
sites$col4 <- sapply(split.col, '[', 4);
if (length(split.col[[1]]) != length(algorithms)) {
stop('Number of algorithms does not match number of columns in sites.txt file');
}
for (i in 1:length(split.col[[1]])) {
sites[, i + sites.original.ncol ] <- sapply(split.col, '[', i);
}
sites$V5 <- NULL;

header <- c('chrom', 'pos', 'ref', 'alt', algorithms);
colnames(sites) <- header
colnames(sites) <- c('chrom', 'pos', 'ref', 'alt', algorithms);

variants <- paste(sites$chrom, sites$pos, sep = '_');
tool.variants <- lapply(sites[, algorithms], function(x) variants[x == 1]);
tool.variants.ordered <- tool.variants[order(lengths(tool.variants), decreasing = TRUE)];
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plot.venn(tool.variants.ordered, args$outfile);
plot.venn(tool.variants, args$outfile);
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