changeset 1:c7db13bd4c85 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ggplotscriptviolin.R	Wed Feb 22 22:36:41 2017 -0500
@@ -0,0 +1,86 @@
+# 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 to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+
+# Import library
+library("getopt")
+library("reshape2")
+library("ggplot2")
+options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
+# Take in trailing command line arguments
+args <- commandArgs(trailingOnly = TRUE)
+
+
+# get options, using the spec as defined by the enclosed list.
+# we read the options from the default: commandArgs(TRUE).
+option_specification = matrix(c(
+  'input', 'i', 2, 'character',
+  'title', 't',2, 'character',
+  'ggfill', 's', 2, 'character',
+  'ggcolor', 'z', 2, 'character',
+  'xlab', 'x', 2, 'character',
+  'ylab', 'y', 2, 'character',
+  'drawquartiles', 'a', 2, 'character',
+  'transform', 'w', 2, 'character',
+  'xaxismin', 'e', 2, 'integer',
+  'xaxismax', 'f', 2, 'integer',
+  'yaxismin', 'g', 2, 'integer',
+  'yaxismax', 'h', 2, 'integer',
+  'scaling', 'b', 2, 'character',
+  'output', 'o', 2, 'character'
+  ), byrow=TRUE, ncol=4);
+
+# Parse options
+options = getopt(option_specification);
+
+
+
+# Print options to see what is going on
+cat("\n input: ",options$input)
+cat("\n title: ",options$title)
+#cat("\n size: ",options$size)
+cat("\n xlab: ",options$xlab)
+cat("\n ylab: ",options$ylab)
+cat("\n output: ",options$output)
+
+
+if(options$scaling == "Automatic"){
+    gg_scaley = NULL
+} else {
+    gg_scaley = ylim(options$yaxismin,options$yaxismax)
+    cat("\n yaxismin: ",options$yaxismin)
+    cat("\n yaxismax: ",options$yaxismax)
+}
+
+
+integrated <- read.csv(options$input,sep='\t',header=TRUE)
+input <- melt(integrated)
+
+
+
+if(options$transform == "log2"){
+    input["value"] <- log2(input["value"])
+}else if(options$transform == "log2plus1"){
+    input["value"] <- log2(input["value"]+1)
+}else if(options$transform == "log10"){
+    input["value"] <- log10(input["value"])
+}else if(options$transform == "log10plus1"){
+    input["value"] <- log10(input["value"]+1)
+    }else{
+}
+
+if(options$drawquartiles == "none"){
+    gg_quartile = NULL
+} else {
+    gg_quartile = c(0.25, 0.5, 0.75)
+}
+
+
+
+ggplot(input,aes(variable,value)) +geom_violin(scale = "area", colour = options$ggcolor, fill = options$ggfill, draw_quantiles = gg_quartile) +
+gg_scaley+theme_bw()+xlab(options$xlab)+ylab(options$ylab)+ggtitle(options$title)
+
+ggsave(file=options$output)