Mercurial > repos > artbio > mutational_patterns

comparison mutational_patterns.R @ 16:31e7a33ecd71 draft

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"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
comparison
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15:8182d1625433 16:31e7a33ecd71
218 218
219 if (!is.na(opt$output_cosmic)[1]) { 219 if (!is.na(opt$output_cosmic)[1]) {
220 pdf(opt$output_cosmic, paper = "special", width = 11.69, height = 11.69) 220 pdf(opt$output_cosmic, paper = "special", width = 11.69, height = 11.69)
221 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small psuedocount to the mutation count matrix 221 pseudo_mut_mat <- mut_mat + 0.0001 # First add a small psuedocount to the mutation count matrix
222 if (opt$cosmic_version == "v2") { 222 if (opt$cosmic_version == "v2") {
223 sp_url <- paste("https://cancer.sanger.ac.uk/cancergenome/assets/", "signatures_probabilities.txt", sep = "") 223 sp_url <- "https://cancer.sanger.ac.uk/signatures/documents/420/COSMIC_v2_SBS_GRCh38.txt"
224 cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) 224 cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE)
225 new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type) 225 new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Type)
226 cancer_signatures <- cancer_signatures[as.vector(new_order), ] 226 cancer_signatures <- cancer_signatures[as.vector(new_order), ]
227 row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type 227 row.names(cancer_signatures) <- cancer_signatures$Type
228 cancer_signatures <- as.matrix(cancer_signatures[, 4:33]) 228 cancer_signatures <- as.matrix(cancer_signatures[, 2:31])
229 colnames(cancer_signatures) <- gsub("Signature.", "", colnames(cancer_signatures)) # shorten signature labels 229 colnames(cancer_signatures) <- gsub("Signature_", "", colnames(cancer_signatures)) # shorten signature labels
230 cosmic_tag <- "Signatures (Cosmic v2, March 2015)" 230 cosmic_tag <- "Signatures (Cosmic v2, March 2015)"
231 cosmic_colors <- col_vector[1:30] 231 cosmic_colors <- col_vector[1:30]
232 names(cosmic_colors) <- colnames(cancer_signatures) 232 names(cosmic_colors) <- colnames(cancer_signatures)
233 } else { 233 } else {
234 sp_url <- "https://raw.githubusercontent.com/ARTbio/startbio/master/sigProfiler_SBS_signatures_2019_05_22.tsv" 234 sp_url <- "https://cancer.sanger.ac.uk/signatures/documents/431/COSMIC_v3_SBS_GRCh38.txt"
235 cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) 235 cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE)
236 new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type) 236 new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Type)
237 cancer_signatures <- cancer_signatures[as.vector(new_order), ] 237 cancer_signatures <- cancer_signatures[as.vector(new_order), ]
238 row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type 238 row.names(cancer_signatures) <- cancer_signatures$Type
239 cancer_signatures <- as.matrix(cancer_signatures[, 4:70]) 239 cancer_signatures <- as.matrix(cancer_signatures[, 2:68])
240 colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels 240 colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels
241 cosmic_tag <- "Signatures (Cosmic v3, May 2019)" 241 cosmic_tag <- "Signatures (Cosmic v3, May 2019)"
242 cosmic_colors <- col_vector[1:67] 242 cosmic_colors <- col_vector[1:67]
243 names(cosmic_colors) <- colnames(cancer_signatures) 243 names(cosmic_colors) <- colnames(cancer_signatures)
244 } 244 }