Mercurial > repos > artbio > mutational_patterns

changeset 19:69f09dff98f9 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit db5fd077ec6c840b7b6eda331820999f85fd7c26"
author artbio
date Sun, 17 Oct 2021 23:05:01 +0000
parents 8d9f31389f33
children a2cb7dc9250a
files mutational_patterns.R mutational_patterns.xml
diffstat 2 files changed, 8 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/mutational_patterns.R	Sun Oct 17 15:51:05 2021 +0000
+++ b/mutational_patterns.R	Sun Oct 17 23:05:01 2021 +0000
@@ -236,7 +236,7 @@
                                            cosmic_urls$cosmic_version == opt$cosmic_version]
         sbs_signatures <- read.table(paste0(opt$tooldir, cosmic_sbs_file),
                                             sep = "\t", header = TRUE)
-        tag <- paste(opt$genome, "COSMIC", opt$cosmic_version, sep = " ")
+        tag <- paste(gsub("BSgenome.Hsapiens.UCSC.", "", opt$genome), "COSMIC", opt$cosmic_version, sep = " ")
     }
     # Prepare user-defined signatures
     if (!is.na(opt$own_signatures)) {
@@ -267,8 +267,6 @@
 
     # Plot mutational profiles of the COSMIC signatures
 
-    # to do: this is largely optional and should be graphically improved anyway
-
     pdf(opt$output_sigpattern, paper = "special", width = 11.69, height = 11.69)
     for (i in head(seq(1, ncol(sbs_signatures), by = 20), -1)) {
         p6 <- plot_96_profile(sbs_signatures[, i:(i + 19)], condensed = TRUE, ymax = 0.3)
@@ -281,6 +279,8 @@
     grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc(ncol(sbs_signatures) / 20) + 1, " of ",
                                                trunc(ncol(sbs_signatures) / 20) + 1, " pages)"),
                                         gp = gpar(fontsize = 12, font = 3)))
+
+
     # Find optimal contribution of COSMIC signatures to reconstruct 96 mutational profiles
     pseudo_mut_mat <- mut_mat + 0.0001 # First add a small pseudocount to the mutation count matrix
     fit_res <- fit_to_signatures(pseudo_mut_mat, sbs_signatures)
@@ -293,7 +293,7 @@
         pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
                geom_bar(stat = "identity", position = "stack") +
                coord_flip() +
-               scale_fill_manual(name = "Cosmic\nSignatures", values = signature_colors[]) +
+               scale_fill_manual(name = tag, values = signature_colors[]) +
                labs(x = "Samples", y = "Absolute contribution") + theme_bw() +
                theme(panel.grid.minor.x = element_blank(),
                      panel.grid.major.x = element_blank(),
@@ -304,7 +304,7 @@
         pc4 <- ggplot(pc4_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
                geom_bar(stat = "identity", position = "fill") +
                coord_flip() +
-               scale_fill_manual(name = "Cosmic\nSignatures", values = signature_colors) +
+               scale_fill_manual(name = tag, values = signature_colors) +
                scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
                labs(x = "Samples", y = "Relative contribution") + theme_bw() +
                theme(panel.grid.minor.x = element_blank(), panel.grid.major.x = element_blank(), legend.position = "right",
@@ -318,7 +318,7 @@
         pc3_data <- merge(pc3_data, metadata_table[, c(1, 3)], by.x = "Sample", by.y = "element_identifier")
         pc3 <- ggplot(pc3_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
                geom_bar(stat = "identity", position = "stack") +
-               scale_fill_manual(name = "Cosmic\nSignatures", values = signature_colors) +
+               scale_fill_manual(name = tag, values = signature_colors) +
                labs(x = "Samples", y = "Absolute contribution") + theme_bw() +
                theme(panel.grid.minor.x = element_blank(),
                      panel.grid.major.x = element_blank(),
@@ -330,7 +330,7 @@
         pc4_data <- merge(pc4_data, metadata_table[, c(1, 3)], by.x = "Sample", by.y = "element_identifier")
         pc4 <- ggplot(pc4_data, aes(x = Sample, y = Contribution, fill = as.factor(Signature))) +
                geom_bar(stat = "identity", position = "fill") +
-               scale_fill_manual(name = "Cosmic\nSignatures", values = signature_colors) +
+               scale_fill_manual(name = tag, values = signature_colors) +
                scale_y_continuous(labels = scales::percent_format(accuracy = 1)) +
                labs(x = "Samples", y = "Relative contribution") + theme_bw() +
                theme(panel.grid.minor.x = element_blank(),
--- a/mutational_patterns.xml	Sun Oct 17 15:51:05 2021 +0000
+++ b/mutational_patterns.xml	Sun Oct 17 23:05:01 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy3">
+<tool id="mutational_patterns" name="Analyse Mutational Patterns/Signatures" version="3.2.0+galaxy4">
     <description>from genomic variations in vcf files</description>
     <requirements>
         <requirement type="package" version="3.2.0=r41hdfd78af_0">bioconductor-mutationalpatterns</requirement>