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1 #!/usr/bin/env Rscript
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2 argspec <- c("
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3
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4 Usage:
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5 gen.matrix.heatmap.R -d <data.file>
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6 Optional:
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7 -o <output_file>
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8 \n\n")
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9 args <- commandArgs(TRUE)
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10 if ( length( args ) == 1 && args =="--help") {
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11 write(argspec, stderr())
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12 q();
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13 }
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14
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15
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16 lib.load.quiet <- function( package ) {
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17 package <- as.character(substitute(package))
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18 suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
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19 }
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20 lib.load.quiet(getopt)
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21 lib.load.quiet( gplots )
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22 lib.load.quiet( amap )
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23 lib.load.quiet( ctc )
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24 if ( any( c( 'flashClust', 'fastcluster' ) %in% installed.packages() ) ) {
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25 if ( 'flashClust' %in% installed.packages() ) {
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26 lib.load.quiet( flashClust )
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27 } else {
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28 if ( 'fastcluster' %in% installed.packages() ) {
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29 lib.load.quiet( fastcluster )
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30 }
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31 }
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32 }
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33
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34
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35 spec <- matrix( c( "dataset", "d", 1, "character",
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36 "reverse.rows", "r", 2, "character",
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37 "image.format", "i", 2, "character",
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38 "output.fname", "o", 2, "character",
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39 "output.report.html", "h", 2, "character",
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40 "output.report.dir", "p", 2, "character",
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41 "output.treeview", "t", 2, "character"
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42 ),
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43 nc=4,
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44 byrow=TRUE
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45 )
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46
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47
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48 opt <- getopt( spec=spec )
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49 if ( is.null( opt$image.format ) ){
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50 opt$image.format <- "png"
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51 } else {
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52 if ( ! opt$image.format %in% c( "pdf", "png" ) ) stop( 'invalid image format specified\n' )
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53 }
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54 if ( is.null( opt$output.report.dir ) ) { opt$output.report.dir <- "report" }
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55 if ( is.null( opt$output.report.html ) ) {
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56 if ( opt$image.format == "pdf" ) opt$output.report.html <- "report/heatmap.pdf"
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57 if ( opt$image.format == "png" ) opt$output.report.html <- "report/index.html"
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58 }
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59 if ( is.null( opt$output.treeview ) ) {
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60 opt$output.treeview <- FALSE
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61 } else {
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62 if ( ! opt$output.treeview %in% c( "no", "yes" ) ) {
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63 stop( "invalid input to output.treeview param", opt$output.treeview, "\n" )
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64 }
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65 ## set to TRUE/FALSE
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66 opt$output.treeview <- ( opt$output.treeview == "yes" )
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67 }
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68 if ( is.null( opt$reverse.rows ) ) {
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69 opt$reverse.rows <- TRUE
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70 } else {
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71 if ( ! opt$reverse.rows %in% c( "no", "yes" ) ) {
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72 stop( "invalid input to reverse.rows param", opt$reverse.rows, "\n" )
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73 }
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74
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75 ## set to TRUE/FALSE
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76 opt$reverse.rows <- ( opt$reverse.rows == "yes" )
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77 }
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78
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79 if ( ( opt$image.format == "png" ) || opt$output.treeview ) {
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80 if ( !file.exists( opt$output.report.dir ) ){
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81 dir.create(opt$output.report.dir, recursive=T)
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82 }
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83 }
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84
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85
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86 data <- as.matrix( read.delim(opt$dataset, row.names=1, check.names=F ) ) ## should load the cl, treecl.res (or partcl.res) and data
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87 hr <- hclust( Dist( data, "euclidean" ) )
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88 row.ddr <- as.dendrogram( hr )
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89 if ( opt$reverse.rows ) row.ddr <- rev( row.ddr )
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90 hc <- hclust( Dist( t( data ), "euclidean" ) )
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91 col.ddr <- as.dendrogram( hc )
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92 hmcols<-colorRampPalette(c("blue","white","red"))(256)
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93
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94 param.list <- list( x=data,
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95 Rowv=row.ddr,
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96 Colv=col.ddr,
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97 dendrogram="both",
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98 trace="none",
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99 col=hmcols,
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100 symbreaks=TRUE,
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101 scale="none",
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102 labRow="",
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103 labCol="",
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104 na.color='grey' ) #,
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105 ##key=FALSE )
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106
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107
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108 if ( opt$image.format == 'png' ) {
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109
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110 png.fname <- file.path( opt$output.report.dir, "cluster.heatmap.png")
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111 plot.dev <- png( png.fname,
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112 width=8.5,
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113 height=11,
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114 units='in',
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115 res=72 )
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116 } else {
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117 pdf.fname <- opt$output.report.html
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118 pdf( opt$output.report.html,
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119 paper="letter" )
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120 }
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121
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122 heatmap.retval <- do.call( "heatmap.2", param.list )
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123 dev.off()
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124
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125 if ( opt$image.format == 'png' ) {
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126 pngs = list.files(path=opt$output.report.dir, patt="png")
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127 html.out <- paste( "<html>",
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128 paste( paste( paste( "<div><img src=\'", pngs, sep="" ), "\'/></div>", sep="" ), collapse=""),
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129 "</html>" )
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130 cat( html.out, file=opt$output.report.html )
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131 }
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132
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133
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134 if ( opt$output.treeview ) {
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135 treeview.fname.stem <- file.path( opt$output.report.dir, "cluster.heatmap")
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136
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137 fnames <- character()
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138 fname <- paste( treeview.fname.stem, ".gtr", sep="" )
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139 r2gtr( hr, file=fname )
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140 fnames <- c( fnames, fname )
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141
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142 fname <- paste( treeview.fname.stem, ".atr", sep="" )
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143 r2atr( hc, file=fname )
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144 fnames <- c( fnames, fname )
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145
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146 fname <- paste( treeview.fname.stem, ".cdt", sep="" )
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147 r2cdt( hr, hc, data, file=fname )
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148 fnames <- c( fnames, fname )
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149
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150 ## jtv file now
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151 jtv.str <- '<DocumentConfig><UrlExtractor/><ArrayUrlExtractor/><Views><View type="Dendrogram" dock="1"><ColorExtractor contrast="2.0"><ColorSet zero="#FFFFFF" down="#0000FF"/></ColorExtractor><ArrayDrawer/><GlobalXMap current="Fill"><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></GlobalXMap><GlobalYMap current="Fill"><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></GlobalYMap><ZoomXMap><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></ZoomXMap><ZoomYMap><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></ZoomYMap><TextView><TextView face="Monospaced" size="14"><GeneSummary/></TextView><TextView face="Monospaced" size="14"><GeneSummary/></TextView><TextView face="Monospaced" size="14"><GeneSummary/></TextView><TextView face="Monospaced" size="14"><GeneSummary/></TextView></TextView><ArrayNameView face="Monospaced" size="14"><ArraySummary included="0"/></ArrayNameView><AtrSummary/><GtrSummary/></View></Views></DocumentConfig>'
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152 fname <- paste( treeview.fname.stem, ".jtv", sep="" )
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153 cat( jtv.str, file=fname )
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154 fnames <- c( fnames, fname )
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155
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156 cmd <- paste( "tar -zcf", opt$output.fname, paste( "--directory=", opt$output.report.dir, sep="" ), paste( basename( fnames ), collapse=" " ) )
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157 system( cmd )
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158 }
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159
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160
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