comparison volcanoplot.R @ 3:6d532d760950 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 16205b1cd782c5a4f7c08af7d4ee50dc5903418b

2:d1d39c72b755

    "label_file", "f", 1, "character",
    "top_num", "t", 1, "integer",
    "title", "T", 1, "character",
    "xlab", "X", 1, "character",
    "ylab", "Y", 1, "character",
    "legend", "L", 1, "character",
    "llabs", "z", 1, "character"),
    byrow=TRUE, ncol=4)
opt <- getopt(spec)

# Below modified from http://www.gettinggeneticsdone.com/2016/01/repel-overlapping-text-labels-in-ggplot2.html

results <- read.delim(opt$input)
results$fdr <- results[, opt$fdr_col]
results$Pvalue <- results[, opt$pval_col]
results$logFC <- results[, opt$lfc_col]
results$labels <- results[, opt$label_col]
label_down <- unlist(strsplit(opt$llabs, split=","))[1]
label_notsig <- unlist(strsplit(opt$llabs, split=","))[2]
label_up <- unlist(strsplit(opt$llabs, split=","))[3]
colours <- setNames(c("cornflowerblue","grey","firebrick"),c(label_down,label_notsig,label_up))

results <- mutate(results, sig=ifelse((fdr<opt$signif_thresh & logFC>opt$lfc_thresh), label_up, ifelse((fdr<opt$signif_thresh & logFC < -opt$lfc_thresh),label_down, label_notsig)))
results <- results[order(results$Pvalue),]
if (!is.null(opt$label_file)) {
    labelfile <- read.delim(opt$label_file)
    # label genes specified in file
    tolabel <- filter(results, labels %in% labelfile[, 1])
} else if (is.null(opt$top_num)) {
    # label all significant genes
    tolabel <- filter(results, sig != label_notsig)
} else if (opt$top_num > 0) {
    # label only top significant genes
    tolabel <- filter(results, sig != label_notsig) %>%
    top_n(n=-opt$top_num, Pvalue)
} else if (opt$top_num == 0) {
    # no labels
    tolabel <- NULL
}

pdf("out.pdf")
p <- ggplot(results, aes(logFC, -log10(Pvalue))) +
    geom_point(aes(col=sig)) +

    p <- p + xlab(opt$xlab)
}
if (!is.null(opt$ylab)) {
    p <- p + ylab(opt$ylab)
}
if (!is.null(opt$legend)) {
    p <- p + labs(colour=opt$legend)
} else {
    p <- p + labs(colour="")
}
if (!is.null(tolabel)) {
    p <- p + geom_label_repel(data=tolabel, aes(label=labels, fill=factor(sig)), colour="white", segment.colour="black", show.legend=FALSE)
}

print(p)
dev.off()

3:6d532d760950

    "label_file", "f", 1, "character",
    "top_num", "t", 1, "integer",
    "title", "T", 1, "character",
    "xlab", "X", 1, "character",
    "ylab", "Y", 1, "character",
    "xmin", "m", 1, "double",
    "xmax", "M", 1, "double",
    "ymax", "W", 1, "double",
    "legend", "L", 1, "character",
    "llabs", "z", 1, "character",
    "boxes", "b", 0, "logical"),
    byrow=TRUE, ncol=4)
opt <- getopt(spec)

# Below modified from http://www.gettinggeneticsdone.com/2016/01/repel-overlapping-text-labels-in-ggplot2.html

results <- read.delim(opt$input)
results$fdr <- results[, opt$fdr_col]
results$Pvalue <- results[, opt$pval_col]
results$logFC <- results[, opt$lfc_col]
results$labels <- as.character(results[, opt$label_col])
label_down <- unlist(strsplit(opt$llabs, split=","))[1]
label_notsig <- unlist(strsplit(opt$llabs, split=","))[2]
label_up <- unlist(strsplit(opt$llabs, split=","))[3]
colours <- setNames(c("cornflowerblue","grey","firebrick"),c(label_down,label_notsig,label_up))

results <- mutate(results, sig=ifelse((fdr<opt$signif_thresh & logFC>opt$lfc_thresh), label_up, ifelse((fdr<opt$signif_thresh & logFC < -opt$lfc_thresh),label_down, label_notsig)))
results <- results[order(results$Pvalue),]
if (!is.null(opt$label_file)) {
    labelfile <- read.delim(opt$label_file, stringsAsFactors=FALSE)
    # label genes specified in file
    results <- mutate(results, labels=ifelse(labels %in% labelfile[, 1], labels, ""))
} else if (is.null(opt$top_num)) {
    # label all significant genes
    results <- mutate(results, labels=ifelse(sig != label_notsig, labels, ""))
} else if (opt$top_num > 0) {
    # label only top significant genes
    top <- filter(results, sig != label_notsig) %>% top_n(n=-opt$top_num, Pvalue)
    results <- mutate(results, labels=ifelse(labels %in% top$labels, labels, ""))
} else if (opt$top_num == 0) {
    # no labels
    results$labels <- NULL
}

pdf("out.pdf")
p <- ggplot(results, aes(logFC, -log10(Pvalue))) +
    geom_point(aes(col=sig)) +

    p <- p + xlab(opt$xlab)
}
if (!is.null(opt$ylab)) {
    p <- p + ylab(opt$ylab)
}
if (!is.null(opt$xmin) & !is.null(opt$xmax)) {
    p <- p + xlim(opt$xmin, opt$xmax)
}
if (!is.null(opt$ymax)) {
    p <- p + ylim(0, opt$ymax)
}
if (!is.null(opt$legend)) {
    p <- p + labs(colour=opt$legend)
} else {
    p <- p + labs(colour="")
}
if (!is.null(results$labels)) {
    if (!is.null(opt$boxes)) {
        p <- p + geom_label_repel(aes(label=labels, fill=sig), segment.colour="black", colour="white", min.segment.length=0, show.legend=FALSE)
    } else {
        p <- p + geom_text_repel(aes(label=labels, col=sig), min.segment.length=0, box.padding=0.3, point.padding=0.3, show.legend=FALSE)
    }
}

print(p)
dev.off()