diff test-data/out.rscript @ 5:44608d0193ed draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit 8464d1b013c316d88b37884be521c0ef50be5623"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/out.rscript	Sun Jun 06 09:12:22 2021 +0000
@@ -0,0 +1,103 @@
+
+# Galaxy settings start ---------------------------------------------------
+
+# setup R error handling to go to stderr
+options(show.error.messages = F, error = function() {cat(geterrmessage(), file = stderr()); q("no", 1, F)})
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+
+# Load packages -----------------------------------------------------------
+
+suppressPackageStartupMessages({
+    library(dplyr)
+    library(ggplot2)
+    library(ggrepel)
+})
+
+
+# Import data  ------------------------------------------------------------
+
+# Check if header is present by checking if P value column is numeric or not
+
+first_line <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpfpemuuun/files/8/3/7/dataset_8374ef6b-02c7-46f1-afc9-408a2a6cbde4.dat', header = FALSE, nrow = 1)
+
+first_pvalue <- first_line[, 3]
+
+if (is.numeric(first_pvalue)) {
+  print("No header row detected")
+  results <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpfpemuuun/files/8/3/7/dataset_8374ef6b-02c7-46f1-afc9-408a2a6cbde4.dat', header = FALSE)
+} else {
+  print("Header row detected")
+  results <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpfpemuuun/files/8/3/7/dataset_8374ef6b-02c7-46f1-afc9-408a2a6cbde4.dat', header = TRUE)
+}
+
+
+# Format data  ------------------------------------------------------------
+
+# Create columns from the column numbers specified
+results <- results %>% mutate(fdr = .[[4]],
+                              pvalue = .[[3]],
+                              logfc = .[[2]],
+                              labels = .[[1]])
+
+# Get names for legend
+down <- unlist(strsplit('Down,Not Sig,Up', split = ","))[1]
+notsig <- unlist(strsplit('Down,Not Sig,Up', split = ","))[2]
+up <- unlist(strsplit('Down,Not Sig,Up', split = ","))[3]
+
+# Set colours
+colours <- setNames(c("cornflowerblue", "grey", "firebrick"), c(down, notsig, up))
+
+# Create significant (sig) column
+results <- mutate(results, sig = case_when(
+                                fdr < 0.05 & logfc > 0.0 ~ up, 
+                                fdr < 0.05 & logfc < -0.0 ~ down, 
+                                TRUE ~ notsig))
+
+
+# Specify genes to label --------------------------------------------------
+labelfile <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmpfpemuuun/files/4/2/f/dataset_42fc8a63-f9cc-435b-9bb3-dd106b708cd9.dat')
+results <- mutate(results, labels = ifelse(labels %in% labelfile[, 1], labels, ""))
+
+
+# Create plot -------------------------------------------------------------
+
+pdf("out.pdf")
+p <- ggplot(results, aes(x = logfc, y = -log10(pvalue))) +
+    geom_point(aes(colour = sig)) +
+    scale_color_manual(values = colours) +
+    scale_fill_manual(values = colours) +
+    theme(panel.grid.major = element_blank(),
+        panel.grid.minor = element_blank(),
+        panel.background = element_blank(),
+        axis.line = element_line(colour = "black"),
+        legend.key = element_blank())
+
+
+
+
+
+
+# Set legend title
+p <- p + labs(colour = "")
+
+# Add gene labels in boxes
+p <- p + geom_label_repel(aes(label = labels, fill = sig), 
+                          segment.colour = "black", 
+                          colour = "white", 
+                          min.segment.length = 0, 
+                          show.legend = FALSE)
+
+print(p)
+dev.off()
+
+
+# Save RData -------------------------------------------------------------
+save.image(file="volcanoplot.RData")
+
+
+# R and Package versions -------------------------------------------------
+sessionInfo()
+