diff ggplotscripthistogram.R @ 31:0d872b4dfca1 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ggplotscripthistogram.R	Tue Apr 11 19:15:18 2017 -0400
@@ -0,0 +1,135 @@
+# 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',
+  'size', 's', 2, 'double',
+  'xlab', 'x', 2, 'character',
+  'ylab', 'y', 2, 'character',
+  'binwidth', 'b', 2, 'double',
+  'xaxismin', 'e', 2, 'integer',
+  'xaxismax', 'f', 2, 'integer',
+  'yaxismin', 'g', 2, 'integer',
+  'yaxismax', 'h', 2, 'integer',
+  'colors', 'q', 2, 'character',
+  'colorscheme', 'z', 2, 'character',
+  'colororder', 'r', 2, 'integer',
+  'facet', 'a', 2, 'character',
+  'transform', 'c', 2, 'character',
+  'woutputdim', 'w', 2, 'integer',
+  'houtputdim', 'd', 2, 'integer',
+  'dim', 'k', 2, 'character',
+  'scaling', 'j', 2, 'character',
+  'legend', 'l', 2, 'character',
+  'density', 'm', 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$size)
+cat("\n transform: ",options$alpha)
+cat("\n xlab: ",options$xlab)
+cat("\n xlab: ",options$xlab)
+cat("\n binwidth: ",options$binwidth)
+cat("\n output: ",options$output)
+
+integrated <- read.csv(options$input,sep='\t',header=TRUE)
+input <- melt(integrated)
+
+#Show/hide legend
+if(options$legend == "yes"){
+    gg_legend = NULL
+} else {
+    gg_legend = theme(legend.position="none")
+}
+
+#density 
+if(options$density == "counts"){
+    gg_density = ggplot(input,aes(value, color=variable))
+    gg_freq = NULL
+}else if(options$density == "nfreq"){
+    gg_density = ggplot(input,aes(value, ..ncount.., color=variable))
+    gg_freq = NULL
+}else if(options$density == "freq"){
+    gg_density = ggplot(input,aes(value, color=variable))
+    gg_freq = aes(y=..count../sum(..count..))
+}else {
+
+}
+
+#Choose between automatically scaled x and y axis or user defined
+if(options$scaling == "Automatic"){
+    gg_scalex = NULL
+    gg_scaley = NULL
+} else {
+    gg_scalex = xlim(options$xaxismin,options$xaxismax)
+    gg_scaley = ylim(options$yaxismin,options$yaxismax)
+    cat("\n xaxismin: ",options$xaxismin)
+    cat("\n xaxismax: ",options$xaxismax)
+    cat("\n yaxismin: ",options$yaxismin)
+    cat("\n yaxismax: ",options$yaxismax)
+}
+
+#Choose dimensions of output pdf
+if(options$dim == "Default"){
+    gg_width = 7
+    gg_height = 7
+} else {
+    gg_width = options$woutputdim
+    gg_height = options$houtputdim 
+}
+
+
+if(options$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$transform == "log10plus1"){
+    input["value"] <- log10(input["value"]+1)
+    }else{
+}
+
+
+if(options$facet == "facet"){
+    gg_facet = facet_wrap(~ variable)
+  } else {
+    gg_facet = NULL
+  }
+
+if(options$colorscheme == "Default"){
+    gg_colorscale = NULL
+  } else {
+    gg_colorscale = scale_color_brewer(palette=options$colors, direction=options$colororder)
+  }
+
+gg_density +
+geom_freqpoly(gg_freq,binwidth=options$binwidth,size=options$size)+gg_facet+gg_colorscale+
+gg_scalex+gg_scaley+theme_bw()+xlab(options$xlab)+ylab(options$ylab)+gg_legend+
+ggtitle(options$title)
+
+ggsave(file=options$output)