Mercurial > repos > artbio > mutational_patterns

comparison mutational_patterns.R @ 15:8182d1625433 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 6ca5597637439c87b61af2dbd6c38089b29eca37"
author artbio
date Sun, 03 Oct 2021 09:29:04 +0000
parents 56c8869a231e
children 31e7a33ecd71
comparison
equal deleted inserted replaced
14:56c8869a231e 15:8182d1625433
182 # Assign signature names 182 # Assign signature names
183 colnames(nmf_res$signatures) <- paste0("NewSig_", 1:opt$newsignum) 183 colnames(nmf_res$signatures) <- paste0("NewSig_", 1:opt$newsignum)
184 rownames(nmf_res$contribution) <- paste0("NewSig_", 1:opt$newsignum) 184 rownames(nmf_res$contribution) <- paste0("NewSig_", 1:opt$newsignum)
185 # Plot the 96-profile of the signatures: 185 # Plot the 96-profile of the signatures:
186 p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE) 186 p5 <- plot_96_profile(nmf_res$signatures, condensed = TRUE)
187 new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ variable, value.var = "value") 187 new_sig_matrix <- reshape2::dcast(p5$data, substitution + context ~ sample, value.var = "freq")
188 new_sig_matrix <- format(new_sig_matrix, scientific = TRUE) 188 new_sig_matrix <- format(new_sig_matrix, scientific = TRUE)
189 write.table(new_sig_matrix, file = opt$sigmatrix, quote = FALSE, row.names = FALSE, sep = "\t") 189 write.table(new_sig_matrix, file = opt$sigmatrix, quote = FALSE, row.names = FALSE, sep = "\t")
190 grid.arrange(p5) 190 grid.arrange(p5)
191 # Visualize the contribution of the signatures in a barplot 191 # Visualize the contribution of the signatures in a barplot
192 pc1 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode = "relative", coord_flip = TRUE) 192 pc1 <- plot_contribution(nmf_res$contribution, nmf_res$signature, mode = "relative", coord_flip = TRUE)
227 row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type 227 row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type
228 cancer_signatures <- as.matrix(cancer_signatures[, 4:33]) 228 cancer_signatures <- as.matrix(cancer_signatures[, 4:33])
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 } else { 233 } else {
233 sp_url <- "https://raw.githubusercontent.com/ARTbio/startbio/master/sigProfiler_SBS_signatures_2019_05_22.tsv" 234 sp_url <- "https://raw.githubusercontent.com/ARTbio/startbio/master/sigProfiler_SBS_signatures_2019_05_22.tsv"
234 cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE) 235 cancer_signatures <- read.table(sp_url, sep = "\t", header = TRUE)
235 new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type) 236 new_order <- match(row.names(pseudo_mut_mat), cancer_signatures$Somatic.Mutation.Type)
236 cancer_signatures <- cancer_signatures[as.vector(new_order), ] 237 cancer_signatures <- cancer_signatures[as.vector(new_order), ]
237 row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type 238 row.names(cancer_signatures) <- cancer_signatures$Somatic.Mutation.Type
238 cancer_signatures <- as.matrix(cancer_signatures[, 4:70]) 239 cancer_signatures <- as.matrix(cancer_signatures[, 4:70])
239 colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels 240 colnames(cancer_signatures) <- gsub("SBS", "", colnames(cancer_signatures)) # shorten signature labels
240 cosmic_tag <- "Signatures (Cosmic v3, May 2019)" 241 cosmic_tag <- "Signatures (Cosmic v3, May 2019)"
241 cosmic_colors <- col_vector[1:67] 242 cosmic_colors <- col_vector[1:67]
243 names(cosmic_colors) <- colnames(cancer_signatures)
242 } 244 }
243 245
244 # Plot mutational profiles of the COSMIC signatures 246 # Plot mutational profiles of the COSMIC signatures
245 if (opt$cosmic_version == "v2") { 247 if (opt$cosmic_version == "v2") {
246 p6 <- plot_96_profile(cancer_signatures, condensed = TRUE, ymax = 0.3) 248 p6 <- plot_96_profile(cancer_signatures, condensed = TRUE, ymax = 0.3)
257 259
258 # Find optimal contribution of COSMIC signatures to reconstruct 96 mutational profiles 260 # Find optimal contribution of COSMIC signatures to reconstruct 96 mutational profiles
259 fit_res <- fit_to_signatures(pseudo_mut_mat, cancer_signatures) 261 fit_res <- fit_to_signatures(pseudo_mut_mat, cancer_signatures)
260 262
261 # Plot contribution barplots 263 # Plot contribution barplots
262 pc3 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "absolute") 264 pc3 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "absolute")
263 pc4 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "relative") 265 pc4 <- plot_contribution(fit_res$contribution, cancer_signatures, coord_flip = T, mode = "relative")
266 if (is.na(opt$levels)[1]) { # if there are NO levels to display in graphs
264 pc3_data <- pc3$data 267 pc3_data <- pc3$data
265 pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) + 268 pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
266 geom_bar(stat = "identity", position = "stack") + 269 geom_bar(stat = "identity", position = "stack") +
267 coord_flip() + 270 coord_flip() +
268 scale_fill_manual(name = "Cosmic\nSignatures", values = cosmic_colors) + 271 scale_fill_manual(name = "Cosmic\nSignatures", values = cosmic_colors) +
280 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) + 283 scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
281 labs(x = "Samples", y = "Relative contribution") + theme_bw() + 284 labs(x = "Samples", y = "Relative contribution") + theme_bw() +
282 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position = "right", 285 theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position = "right",
283 text = element_text(size = 8), 286 text = element_text(size = 8),
284 axis.text.x = element_text(angle = 90, hjust = 1)) 287 axis.text.x = element_text(angle = 90, hjust = 1))
288 }
285 ##### 289 #####
286 # ggplot2 alternative 290 # ggplot2 alternative
287 if (!is.na(opt$levels)[1]) { # if there are levels to display in graphs 291 if (!is.na(opt$levels)[1]) { # if there are levels to display in graphs
288 pc3_data <- pc3$data 292 pc3_data <- pc3$data
289 pc3_data <- merge(pc3_data, metadata_table[, c(1, 3)], by.x = "Sample", by.y = "element_identifier") 293 pc3_data <- merge(pc3_data, metadata_table[, c(1, 3)], by.x = "Sample", by.y = "element_identifier")
340 worklist[[i]] <- worklist[[i]][1:opt$signum, ] 344 worklist[[i]] <- worklist[[i]][1:opt$signum, ]
341 worklist[[i]] <- worklist[[i]][, -length(as.data.frame(worklist[[i]]))] 345 worklist[[i]] <- worklist[[i]][, -length(as.data.frame(worklist[[i]]))]
342 } 346 }
343 worklist <- as.data.frame(melt(worklist)) 347 worklist <- as.data.frame(melt(worklist))
344 worklist[, 2] <- paste0(worklist[, 4], " - ", worklist[, 2]) 348 worklist[, 2] <- paste0(worklist[, 4], " - ", worklist[, 2])
345 head(worklist)
346 } 349 }
347 350
348 colnames(worklist) <- c("signature", "sample", "value", "level") 351 colnames(worklist) <- c("signature", "sample", "value", "level")
349 worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value = value / sum(value) * 100)) 352 worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value = value / sum(value) * 100))
350 worklist$pos <- cumsum(worklist$value) - worklist$value / 2 353 worklist$pos <- cumsum(worklist$value) - worklist$value / 2
354 geom_bar(width = 1, stat = "identity") + 357 geom_bar(width = 1, stat = "identity") +
355 geom_text(aes(label = label), position = position_stack(vjust = 0.5), color = "black", size = 3) + 358 geom_text(aes(label = label), position = position_stack(vjust = 0.5), color = "black", size = 3) +
356 coord_polar("y", start = 0) + facet_wrap(.~sample) + 359 coord_polar("y", start = 0) + facet_wrap(.~sample) +
357 labs(x = "", y = "Samples", fill = cosmic_tag) + 360 labs(x = "", y = "Samples", fill = cosmic_tag) +
358 scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"), 361 scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"),
359 values = cosmic_colors[as.numeric(levels(factor(worklist$label)))]) + 362 values = cosmic_colors[levels(worklist$signature)]) +
360 theme(axis.text = element_blank(), 363 theme(axis.text = element_blank(),
361 axis.ticks = element_blank(), 364 axis.ticks = element_blank(),
362 panel.grid = element_blank()) 365 panel.grid = element_blank())
363 grid.arrange(p7) 366 grid.arrange(p7)
364 367