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3
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1 # Setup R error handling to go to stderr
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2 options(show.error.messages=F, error=function(){cat(geterrmessage(),file=stderr());q("no",1,F)})
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2
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3
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3
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4 # We need to not crash galaxy with an UTF8 error on German LC settings.
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5 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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2
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6
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7
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3
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8 # Import library
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9 library("getopt")
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10 library("RColorBrewer")
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11 library("gplots")
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12 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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13 # Take in trailing command line arguments
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14 args <- commandArgs(trailingOnly = TRUE)
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2
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15
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16
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3
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17 # get options, using the spec as defined by the enclosed list.
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18 # we read the options from the default: commandArgs(TRUE).
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19 option_specification = matrix(c(
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20 'input', 'i', 2, 'character',
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8
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21 'title', 't', 2, 'character',
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3
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22 'transform', 'c', 2, 'character',
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8
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23 'key', 'k', 2, 'character',
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10
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24 'colorscheme', 'z', 2, 'character',
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13
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25 'cluster', 'b', 2, 'character',
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26 'labels', 'a', 2, 'character',
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14
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27 'scale', 'd', 2, 'character',
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3
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28 'output', 'o', 2, 'character'
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29 ), byrow=TRUE, ncol=4);
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2
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30
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3
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31 # Parse options
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32 options = getopt(option_specification);
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2
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33
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34
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35
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3
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36 # Print options to see what is going on
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37 cat("\n input: ",options$input)
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38 cat("\n title: ",options$title)
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39 cat("\n output: ",options$output)
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2
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40
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3
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41 input <- read.delim(options$input,sep='\t',header=TRUE)
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2
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42
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25
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43 mat_input <- data.matrix(input[,2:ncol(input)])
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44 rownames(mat_input) <- input[,1]
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2
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45
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3
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46 if(options$transform == "none"){
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47 linput <- mat_input
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48 }else if(options$transform == "log2"){
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49 linput <- log2(mat_input)
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50 }else if(options$transform == "log2plus1"){
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51 linput <- log2(mat_input+1)
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52 }else if(options$transform == "log10"){
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53 linput <- log10(mat_input)
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54 }else if(options$transform == "log10plus1"){
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55 linput <- log10(mat_input+1)
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56 }else{
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57 }
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2
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58
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13
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59 if(options$colorscheme == "whrd"){
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10
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60 colorscale = colfunc <- colorRampPalette(c("white", "red"))
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13
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61 } else if(options$colorscheme == "whblu"){
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62 colorscale = colfunc <- colorRampPalette(c("white", "blue"))
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63 }else if(options$colorscheme == "blwhre"){
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10
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64 colorscale = colfunc <- colorRampPalette(c("blue","white", "red"))
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13
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65 }else{
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10
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66 }
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2
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67
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68
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13
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69 if(options$cluster== "Default"){
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70 hclust_fun = function(x) hclust(x, method="complete")
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71 dist_fun = function(x) dist(x, method="maximum")
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15
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72 dclust = distfun=dist_fun
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73 hclust = hclustfun=hclust_fun
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25
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74 dend = NULL
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13
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75 }else{
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15
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76 dclust = NULL
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77 hclust = NULL
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25
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78 dend = dendrogram="none"
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13
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79 }
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80
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81 if(options$labels== "both"){
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17
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82 rlabs = NULL
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83 clabs = NULL
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13
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84 }else if(options$labels== "rows"){
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17
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85 rlabs = NULL
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86 clabs = labCol=FALSE
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13
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87 }else if(options$labels== "columns"){
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17
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88 rlabs = labRow=FALSE
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89 clabs = NULL
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13
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90 }else if(options$labels== "none"){
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17
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91 rlabs = labRow=FALSE
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92 clabs = labCol=FALSE
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13
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93 } else{
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94 }
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95
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96
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97
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2
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98
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3
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99 pdf(file="Rplot.pdf")
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10
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100 colorscale
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3
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101 heatmap.2(linput,
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25
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102 dclust, hclust, dend, scale = options$scale, rlabs, clabs,
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19
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103 col=colfunc(50), trace="none", density.info = "none", margins=c(8,2),
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8
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104 main = options$title, key.xlab= options$key, keysize=1)
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3
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105 dev.off()
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