# HG changeset patch # User moheydarian # Date 1491952494 14400 # Node ID 68a008225c513b08ae0ef829584d4ee2151b08e5 # Parent 1d1518b029d1a1318917b553169798ee7c570071 Deleted selected files diff -r 1d1518b029d1 -r 68a008225c51 ggplot_histogram.xml --- a/ggplot_histogram.xml Tue Apr 11 18:35:55 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,192 +0,0 @@ - - - r-getopt - r-ggplot2 - r-reshape2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -@misc{renameTODO, - author = {TODO, FirstTODO}, - year = {TODO}, - title = {TODO}, - url = {under construction}, -} - - diff -r 1d1518b029d1 -r 68a008225c51 ggplotscripthistogram.R --- a/ggplotscripthistogram.R Tue Apr 11 18:35:55 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,135 +0,0 @@ -# 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)