comparison mutational_patterns.R @ 19:69f09dff98f9 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mutational_patterns commit db5fd077ec6c840b7b6eda331820999f85fd7c26"

18:8d9f31389f33

        cosmic_urls <- read.delim(paste0(opt$tooldir, "cosmic_urls.tsv"), sep = "\t", header = TRUE)
        cosmic_sbs_file <- cosmic_urls$url[cosmic_urls$genome == opt$genome &
                                           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$cosmic_version, sep = " ")
    }
    # Prepare user-defined signatures
    if (!is.na(opt$own_signatures)) {
        sbs_signatures <- read.table(opt$own_signatures, sep = "\t", header = TRUE)
        tag <- paste(opt$genome, "User-Defined Signatures", sep = " ")

    sbs_signatures <- as.matrix(sbs_signatures)


    # 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)
        grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc((i + 1) / 20) + 1, " of ",
                                               trunc(ncol(sbs_signatures) / 20) + 1, " pages)"),

    p6 <- plot_96_profile(sbs_signatures[, (trunc(ncol(sbs_signatures) / 20) * 20):(ncol(sbs_signatures))],
                          condensed = TRUE, ymax = 0.3)
    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)

    # Plot contribution barplots

    if (is.na(opt$levels)[1]) {  # if there are NO levels to display in graphs
        pc3_data <- pc3$data
        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[]) +
               labs(x = "Samples", y = "Absolute contribution") + theme_bw() +
               theme(panel.grid.minor.x = element_blank(),
                     panel.grid.major.x = element_blank(),
                     legend.position = "right",
                     text = element_text(size = 8),
                     axis.text.x = element_text(angle = 90, hjust = 1))
        pc4_data <- pc4$data
        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_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",
                     text = element_text(size = 8),
                     axis.text.x = element_text(angle = 90, hjust = 1))

    if (!is.na(opt$levels)[1]) {  # if there are levels to display in graphs
        pc3_data <- pc3$data
        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) +
               labs(x = "Samples", y = "Absolute contribution") + theme_bw() +
               theme(panel.grid.minor.x = element_blank(),
                     panel.grid.major.x = element_blank(),
                     legend.position = "right",
                     text = element_text(size = 8),

               facet_grid(~level, scales = "free_x", space = "free")
        pc4_data <- pc4$data
        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_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",

19:69f09dff98f9

        cosmic_urls <- read.delim(paste0(opt$tooldir, "cosmic_urls.tsv"), sep = "\t", header = TRUE)
        cosmic_sbs_file <- cosmic_urls$url[cosmic_urls$genome == opt$genome &
                                           cosmic_urls$cosmic_version == opt$cosmic_version]
        sbs_signatures <- read.table(paste0(opt$tooldir, cosmic_sbs_file),
                                            sep = "\t", header = TRUE)
        tag <- paste(gsub("BSgenome.Hsapiens.UCSC.", "", opt$genome), "COSMIC", opt$cosmic_version, sep = " ")
    }
    # Prepare user-defined signatures
    if (!is.na(opt$own_signatures)) {
        sbs_signatures <- read.table(opt$own_signatures, sep = "\t", header = TRUE)
        tag <- paste(opt$genome, "User-Defined Signatures", sep = " ")

    sbs_signatures <- as.matrix(sbs_signatures)


    # Plot mutational profiles of the COSMIC signatures

    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)
        grid.arrange(p6, top = textGrob(paste0(tag, " profiles (", trunc((i + 1) / 20) + 1, " of ",
                                               trunc(ncol(sbs_signatures) / 20) + 1, " pages)"),

    p6 <- plot_96_profile(sbs_signatures[, (trunc(ncol(sbs_signatures) / 20) * 20):(ncol(sbs_signatures))],
                          condensed = TRUE, ymax = 0.3)
    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)

    # Plot contribution barplots

    if (is.na(opt$levels)[1]) {  # if there are NO levels to display in graphs
        pc3_data <- pc3$data
        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 = 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(),
                     legend.position = "right",
                     text = element_text(size = 8),
                     axis.text.x = element_text(angle = 90, hjust = 1))
        pc4_data <- pc4$data
        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 = 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",
                     text = element_text(size = 8),
                     axis.text.x = element_text(angle = 90, hjust = 1))

    if (!is.na(opt$levels)[1]) {  # if there are levels to display in graphs
        pc3_data <- pc3$data
        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 = 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(),
                     legend.position = "right",
                     text = element_text(size = 8),

               facet_grid(~level, scales = "free_x", space = "free")
        pc4_data <- pc4$data
        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 = 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",