Mercurial > repos > artbio > mutational_patterns
changeset 8:e0dad46148bf draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit 75fd87e806f9bee2f6ff7fcd3834e55eb21d8710"
| author | artbio |
|---|---|
| date | Mon, 19 Oct 2020 07:47:24 +0000 |
| parents | 34626b2b9907 |
| children | 4ff3c984523b |
| files | mutational_patterns.R mutational_patterns.xml test-data/cosmic_output1.pdf test-data/cosmic_output2.pdf |
| diffstat | 4 files changed, 52 insertions(+), 26 deletions(-) [+] |
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--- a/mutational_patterns.R Fri Oct 16 10:00:41 2020 +0000 +++ b/mutational_patterns.R Mon Oct 19 07:47:24 2020 +0000 @@ -110,12 +110,16 @@ # Load the VCF files into a GRangesList: vcfs <- read_vcfs_as_granges(vcf_paths, element_identifiers, ref_genome) +library(plyr) if (!is.na(opt$levels)[1]) { # manage levels if there are levels_table <- read.delim(opt$levels, header=FALSE, col.names=c("element_identifier","level")) - library(plyr) - metadata_table <- join(vcf_table, levels_table, by = "element_identifier") - tissue <- as.vector(metadata_table$level) + } else { + levels_table <- data.frame(element_identifier=vcf_table$element_identifier, + level=rep("nolabels", length(vcf_table$element_identifier))) } +metadata_table <- join(vcf_table, levels_table, by = "element_identifier") +tissue <- as.vector(metadata_table$level) +detach(package:plyr) ##### This is done for any section ###### mut_mat <- mut_matrix(vcf_list = vcfs, ref_genome = ref_genome) @@ -130,7 +134,7 @@ # mutation spectrum, total or by sample - if (is.na(opt$levels)[1]) { + if (length(levels(factor(levels_table$level))) == 1) { # (is.na(opt$levels)[1]) p1 <- plot_spectrum(type_occurrences, CT = TRUE, legend=TRUE) plot(p1) } else { @@ -287,28 +291,49 @@ # Combine the two plots: grid.arrange(pc3, pc4, top = textGrob("Absolute and Relative Contributions of Cosmic signatures to mutational patterns",gp=gpar(fontsize=12,font=3))) - # Select signatures with some contribution (above a threshold) - threshold <- tail(sort(unlist(rowSums(fit_res$contribution), use.names = FALSE)), opt$signum)[1] - select <- which(rowSums(fit_res$contribution) >= threshold) # ensure opt$signum best signatures in samples are retained, the others discarded - - ## pie charts of comic signatures contributions in samples - sig_data_pie <- as.data.frame(t(head(fit_res$contribution[select,]))) - colnames(sig_data_pie) <- gsub("nature", "", colnames(sig_data_pie)) - sig_data_pie_percents <- sig_data_pie / (apply(sig_data_pie,1,sum)) * 100 - sig_data_pie_percents$sample <- rownames(sig_data_pie_percents) + #### pie charts of comic signatures contributions in samples ### library(reshape2) - melted_sig_data_pie_percents <-melt(data=sig_data_pie_percents) - melted_sig_data_pie_percents$label <- sub("Sig.", "", melted_sig_data_pie_percents$variable) - melted_sig_data_pie_percents$pos <- cumsum(melted_sig_data_pie_percents$value) - melted_sig_data_pie_percents$value/2 - p7 <- ggplot(melted_sig_data_pie_percents, aes(x="", y=value, group=variable, fill=variable)) + - geom_bar(width = 1, stat = "identity") + - geom_text(aes(label = label), position = position_stack(vjust = 0.5), color="black", size=3) + - coord_polar("y", start=0) + facet_wrap(~ sample) + - labs(x="", y="Samples", fill = cosmic_tag) + - scale_fill_manual(name = paste0(length(select), " most contributing\nSignatures"), values = cosmic_colors[select]) - theme(axis.text = element_blank(), - axis.ticks = element_blank(), - panel.grid = element_blank()) + library(dplyr) + if (length(levels(factor(levels_table$level))) < 2) { + fit_res_contrib <- as.data.frame(fit_res$contribution) + worklist <- cbind(signature=rownames(fit_res$contribution), + level=rep("nolabels", length(fit_res_contrib[,1])), + fit_res_contrib, + sum=rowSums(fit_res_contrib)) + worklist <- worklist[order(worklist[ ,"sum"], decreasing = T), ] + worklist <- worklist[1:opt$signum,] + worklist <- worklist[ , -length(worklist[1,])] + worklist <- melt(worklist) + worklist <- worklist[,c(1,3,4,2)] + } else { + worklist <- list() + for (i in levels(factor(levels_table$level))) { + fit_res$contribution[,levels_table$element_identifier[levels_table$level == i]] -> worklist[[i]] + sum <- rowSums(as.data.frame(worklist[[i]])) + worklist[[i]] <- cbind(worklist[[i]], sum) + worklist[[i]] <- worklist[[i]][order(worklist[[i]][ ,"sum"], decreasing = T), ] + worklist[[i]] <- worklist[[i]][1:opt$signum,] + worklist[[i]] <- worklist[[i]][ , -length(as.data.frame(worklist[[i]]))] + } + worklist <- as.data.frame(melt(worklist)) + } + + colnames(worklist) <- c("signature", "sample", "value", "level") + print(worklist) + worklist <- as.data.frame(worklist %>% group_by(sample) %>% mutate(value=value/sum(value)*100)) + worklist$pos <- cumsum(worklist$value) - worklist$value/2 + worklist$label <- factor(worklist$signature) + worklist$signature <- factor(worklist$signature) + p7 <- ggplot(worklist, aes(x="", y=value, group=signature, fill=signature)) + + geom_bar(width = 1, stat = "identity") + + geom_text(aes(label = label), position = position_stack(vjust = 0.5), color="black", size=3) + + coord_polar("y", start=0) + facet_wrap(~ sample) + + labs(x="", y="Samples", fill = cosmic_tag) + + scale_fill_manual(name = paste0(opt$signum, " most contributing\nsignatures\n(in each label/tissue)"), + values = cosmic_colors[as.numeric(levels(factor(worklist$label)))]) + + theme(axis.text = element_blank(), + axis.ticks = element_blank(), + panel.grid = element_blank()) grid.arrange(p7) # Plot relative contribution of the cancer signatures in each sample as a heatmap with sample clustering
--- a/mutational_patterns.xml Fri Oct 16 10:00:41 2020 +0000 +++ b/mutational_patterns.xml Mon Oct 19 07:47:24 2020 +0000 @@ -1,4 +1,4 @@ -<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy8"> +<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="2.0.0+galaxy9"> <description>from genomic variations in vcf files</description> <requirements> <requirement type="package" version="2.0.0=r40_0">bioconductor-mutationalpatterns</requirement> @@ -231,6 +231,7 @@ <param name="signum" value="3" /> <output name="cosmic" file="cosmic_output1.pdf" compare="sim_size" ftype="pdf"/> </test> + <!-- cosmic signature on single sample --> <test> <param name="vcfs"> <collection type="list">