Mercurial > repos > artbio > mutational_patterns
changeset 9:4ff3c984523b draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 109570d3d5f2c232d3bc976590295c1b83bfc9c3"
| author | artbio |
|---|---|
| date | Mon, 19 Oct 2020 14:55:54 +0000 |
| parents | e0dad46148bf |
| children | 59c0e2a7965c |
| files | mutational_patterns.R mutational_patterns.xml test-data/cosmic_output1.pdf test-data/cosmic_output2.pdf |
| diffstat | 4 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/mutational_patterns.R Mon Oct 19 07:47:24 2020 +0000 +++ b/mutational_patterns.R Mon Oct 19 14:55:54 2020 +0000 @@ -316,10 +316,11 @@ worklist[[i]] <- worklist[[i]][ , -length(as.data.frame(worklist[[i]]))] } worklist <- as.data.frame(melt(worklist)) + worklist[,2] <- paste0(worklist[,2], " - ", worklist[,4]) + head(worklist) } colnames(worklist) <- c("signature", "sample", "value", "level") - print(worklist) worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value=value/sum(value)*100)) worklist$pos <- cumsum(worklist$value) - worklist$value/2 worklist$label <- factor(worklist$signature)
--- a/mutational_patterns.xml Mon Oct 19 07:47:24 2020 +0000 +++ b/mutational_patterns.xml Mon Oct 19 14:55:54 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy9"> +<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy10"> <description>from genomic variations in vcf files</description> <requirements> <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement>