changeset 1:37e17dfc9add draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ggplotpointscript.R	Fri Dec 02 15:33:56 2016 -0500
@@ -0,0 +1,230 @@
+#TO ACCOMPANY ggplot_point.xml version 0.1.2
+# 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("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',
+  'xplot', 'z', 2, 'integer',
+  'yplot', 'j', 2, 'integer',
+  'xaxismin', 'e', 2, 'integer',
+  'xaxismax', 'f', 2, 'integer',
+  'yaxismin', 'g', 2, 'integer',
+  'yaxismax', 'h', 2, 'integer',
+  'alpha', 'a', 2, 'double',
+  'points', 'p', 2, 'character',
+  'theme', 'l', 2, 'character',
+  'scaling', 'b', 2, 'character',
+  'transform', 'w', 2, 'character',
+  'dim', 'k', 2, 'character',
+  'woutputdim', 'c', 2, 'integer',
+  'houtputdim', 'd', 2, 'integer',
+  'factor', 'n', 2, 'character',
+  'factorcol', 'm', 2, 'integer',
+  'colors', 'q', 2, 'character', 
+  'colororder', 'r', 2, 'integer', 
+  'pointcolor', 'u', 2, 'character', 
+  'axistitlecust', 'v', 2, 'character',
+  'axistitlecolor', '1', 2, 'character',
+  'axistitlesize', '2', 2, 'integer',
+  'axistitleface', '3', 2, 'character',
+  'axistextcust', '4', 2, 'character',
+  'axistextcolor', '5', 2, 'character',
+  'axistextsize', '6', 2, 'integer',
+  'axistextface', '7', 2, 'character',
+  'plottitlecust', '8', 2, 'character',
+  'plottitlecolor', '9', 2, 'character',
+  'plottitlesize', '10', 2, 'integer',
+  'plottitleface', '11', 2, 'character',
+  'gridlinecust', '12', 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 xlab: ",options$xlab)
+cat("\n ylab: ",options$ylab)
+cat("\n points: ",options$points)
+cat("\n theme: ",options$theme)
+cat("\n scaling: ",options$scaling)
+cat("\n transform: ",options$transform)
+
+
+
+#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$yaxismax)
+}
+
+# Choose theme for plot
+if(options$theme == "bw"){
+    gg_theme = theme_bw()
+} else {
+    gg_theme = NULL
+}
+
+#Choose dimensions of output pdf
+if(options$dim == "Default"){
+    gg_width = 7
+    gg_height = 7
+} else {
+    gg_width = options$woutputdim
+    gg_height = options$houtputdim 
+}
+
+input <-read.table(options$input, check.names=TRUE, header=TRUE, row.names=NULL)
+
+#renaming columns so ggplot can use them
+names(input)[options$xplot] <- "xcol"
+names(input)[options$yplot] <- "ycol"
+
+#choosing whether to plot data as multiple groups on one plot(factoring) OR multiple groups on different plots
+if(options$factor == "Multiple"){
+     gg_facet = facet_wrap( ~ factor)
+     gg_factor = NULL
+     color_scale = NULL
+          
+          if(options$points == "Default"){
+            gg_point = geom_point(size=1, alpha=1, gg_factor)
+        } else {
+            gg_point = geom_point(size=options$size, alpha=options$alpha, colour=options$pointcolor)
+            cat("\n size: ",options$size)
+            cat("\n alpha: ",options$alpha)
+            cat("\n pointcolor: ",options$pointcolor)
+        }
+
+    names(input)[options$factorcol] <- "factor"
+   
+    cat("\n factor: ",options$factor)
+    cat("\n factorcol: ",options$factorcol)
+} else if(options$factor == "Single"){
+    gg_facet = NULL
+    gg_factor = aes(colour=factor(factor))
+
+          if(options$points == "Default"){
+            gg_point = geom_point(size=1, alpha=1, gg_factor)
+        } else {
+            gg_point = geom_point(size=options$size, alpha=options$alpha, gg_factor)
+            cat("\n size: ",options$size)
+            cat("\n alpha: ",options$alpha)
+            cat("\n pointcolor: ",options$pointcolor)
+        }
+
+      if(options$colors == "Default"){
+          color_scale = scale_colour_hue(direction=options$colororder)
+      } else {
+          color_scale = scale_color_brewer(palette=options$colors, direction=options$colororder)
+      }
+
+    names(input)[options$factorcol] <- "factor"
+    
+    cat("\n factor: ",options$factor)
+    cat("\n factorcol: ",options$factorcol)
+    cat("\n color_scale: ",options$colors)
+    cat("\n color_order: ",options$colororder)
+} else{
+      gg_facet = NULL
+      gg_factor = NULL
+      color_scale = NULL
+
+        if(options$points == "Default"){
+            gg_point = geom_point(size=1, alpha=1, gg_factor)
+        } else {
+            gg_point = geom_point(size=options$size, alpha=options$alpha, colour=options$pointcolor)
+            cat("\n size: ",options$size)
+            cat("\n alpha: ",options$alpha)
+            cat("\n pointcolor: ",options$pointcolor)
+        }    
+}
+
+
+#Selecting whether or not to log transform data
+if(options$transform == "log2"){
+    input[, options$xplot] <- log2(input[options$xplot])
+    input[, options$yplot] <- log2(input[options$yplot])
+}else if(options$transform == "log2plus1"){
+    input[, options$xplot] <- log2(input[options$xplot]+1)
+    input[, options$yplot] <- log2(input[options$yplot]+1)
+}else if(options$transform == "log10"){
+    input[, options$xplot] <- log10(input[options$xplot])
+    input[, options$yplot] <- log10(input[options$yplot])
+}else if(options$transform == "log10plus1"){
+    input[, options$xplot] <- log10(input[options$xplot]+1)
+    input[, options$yplot] <- log10(input[options$yplot]+1)
+    }else{
+}
+
+
+#axis label custization
+if(options$axistitlecust == "Default"){
+    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))
+} else {
+    gg_axistitle = theme(axis.title = element_text(color = options$axistitlecolor, size = options$axistitlesize, face = options$axistitleface))
+}
+
+
+#axis text(tick) custization
+if(options$axistextcust == "Default"){
+    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))
+} else {
+    gg_axistext = theme(axis.text = element_text(color = options$axistextcolor, size = options$axistextsize, face = options$axistextface))
+}
+
+
+#plot title custimization
+if(options$plottitlecust == "Default"){
+    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))
+} else {
+    gg_plottitle = theme(plot.title = element_text(color = options$plottitlecolor, size = options$plottitlesize, face = options$plottitleface))
+}
+
+#grid line customization
+if(options$gridlinecust == "Default"){
+    gg_gridline = NULL
+} else if(options$gridlinecust == "hidemajor"){
+    gg_gridline = theme(panel.grid.major = element_blank())
+} else if(options$gridlinecust == "hideminor"){
+    gg_gridline = theme(panel.grid.minor = element_blank())
+} else if(options$gridlinecust == "hideboth"){
+    gg_gridline = theme(panel.grid.minor = element_blank(), panel.grid.major = element_blank())
+} else {
+}
+
+
+#this is the actual ggplot command to make the final plot(s)
+ggplot(input, aes(xcol,ycol))+gg_point+gg_facet+
+gg_theme+gg_scalex+gg_scaley+color_scale+ggtitle(options$title)+xlab(options$xlab)+ylab(options$ylab)+
+gg_axistitle+gg_axistext+gg_plottitle+gg_gridline
+
+ggsave(file=options$output, width=gg_width, height=gg_height)