diff test-data/out.rscript @ 6:83c573f2e73c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/volcanoplot commit e880a5736a65605ae8a38ca9bc6f17c92c798ccd"

--- a/test-data/out.rscript	Sun Jun 06 09:12:22 2021 +0000
+++ b/test-data/out.rscript	Thu Jun 10 08:38:12 2021 +0000
@@ -7,6 +7,7 @@
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 
+# Galaxy settings end -----------------------------------------------------
 
 # Load packages -----------------------------------------------------------
 
@@ -19,19 +20,7 @@
 
 # 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)
-}
+results <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmprh4qip75/files/d/2/2/dataset_d2255b46-f0f6-4900-8b9e-bd352e34f303.dat', header = TRUE)
 
 
 # Format data  ------------------------------------------------------------
@@ -52,52 +41,57 @@
 
 # Create significant (sig) column
 results <- mutate(results, sig = case_when(
-                                fdr < 0.05 & logfc > 0.0 ~ up, 
-                                fdr < 0.05 & logfc < -0.0 ~ down, 
+                                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')
+
+# Import file with genes of interest
+labelfile <- read.delim('/private/var/folders/zn/m_qvr9zd7tq0wdtsbq255f8xypj_zg/T/tmprh4qip75/files/5/e/5/dataset_5e5b8fb0-bf65-438e-9b5b-03a540d9aa5d.dat', header = TRUE)
+
+# Label the genes of interest in results table
 results <- mutate(results, labels = ifelse(labels %in% labelfile[, 1], labels, ""))
 
 
+
 # Create plot -------------------------------------------------------------
 
-pdf("out.pdf")
-p <- ggplot(results, aes(x = logfc, y = -log10(pvalue))) +
+# Open file to save plot as PDF
+pdf("volcano_plot.pdf")
+
+# Set up base plot
+p <- ggplot(data = 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())
 
+# Add gene labels
+p <- p + geom_text_repel(data = filter(results, labels != ""), aes(label = labels),
+                         min.segment.length = 0,
+                         max.overlaps = Inf,
+                         show.legend = FALSE)
+
 
 
 
 
 
 # Set legend title
-p <- p + labs(colour = "")
+p <- p + theme(legend.title = element_blank())
 
-# 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 plot
+print(p)
 
-print(p)
+# Close PDF graphics device
 dev.off()
 
 
-# Save RData -------------------------------------------------------------
-save.image(file="volcanoplot.RData")
-
-
 # R and Package versions -------------------------------------------------
 sessionInfo()