Mercurial > repos > artbio > mutational_patterns
diff mutational_patterns.R @ 16:31e7a33ecd71 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 9deb533aabc9dc24bb88b98c57e242785142df75"
| author | artbio |
|---|---|
| date | Mon, 04 Oct 2021 00:35:06 +0000 |
| parents | 8182d1625433 |
| children | 8c6ee1c2248f |
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--- a/mutational_patterns.R Sun Oct 03 09:29:04 2021 +0000 +++ b/mutational_patterns.R Mon Oct 04 00:35:06 2021 +0000 @@ -220,23 +220,23 @@ pdf(opt$output_cosmic, paper = "special", width = 11.69, height = 11.69) pseudo_mut_mat <- mut_mat + 0.0001 # First add a small psuedocount to the mutation count matrix if (opt$cosmic_version == "v2") { - sp_url <- paste("https://cancer.sanger.ac.uk/cancergenome/assets/", "signatures_probabilities.txt", sep = "") + sp_url <- "https://cancer.sanger.ac.uk/signatures/documents/420/COSMIC_v2_SBS_GRCh38.txt" cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) - new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type) + new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Type) cancer_signatures <- cancer_signatures[as.vector(new_order), ] - row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type - cancer_signatures <- as.matrix(cancer_signatures[, 4:33]) - colnames(cancer_signatures) <- gsub("Signature.", "", colnames(cancer_signatures)) # shorten signature labels + row.names(cancer_signatures) <- cancer_signatures$Type + cancer_signatures <- as.matrix(cancer_signatures[, 2:31]) + colnames(cancer_signatures) <- gsub("Signature_", "", colnames(cancer_signatures)) # shorten signature labels cosmic_tag <- "Signatures (Cosmic v2, March 2015)" cosmic_colors <- col_vector[1:30] names(cosmic_colors) <- colnames(cancer_signatures) } else { - sp_url <- "https://raw.githubusercontent.com/ARTbio/startbio/master/sigProfiler_SBS_signatures_2019_05_22.tsv" + sp_url <- "https://cancer.sanger.ac.uk/signatures/documents/431/COSMIC_v3_SBS_GRCh38.txt" cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) - new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type) + new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Type) cancer_signatures <- cancer_signatures[as.vector(new_order), ] - row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type - cancer_signatures <- as.matrix(cancer_signatures[, 4:70]) + row.names(cancer_signatures) <- cancer_signatures$Type + cancer_signatures <- as.matrix(cancer_signatures[, 2:68]) colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels cosmic_tag <- "Signatures (Cosmic v3, May 2019)" cosmic_colors <- col_vector[1:67]