diff cluster.tools/gen.matrix.heatmap.R @ 0:0decf3fd54bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/gen.matrix.heatmap.R	Thu Feb 28 01:45:39 2013 -0500
@@ -0,0 +1,160 @@
+#!/usr/bin/env Rscript
+argspec <- c("
+
+        Usage: 
+                gen.matrix.heatmap.R -d <data.file> 
+        Optional:
+                            -o <output_file>
+                \n\n")
+args <- commandArgs(TRUE)
+if ( length( args ) == 1 && args =="--help") { 
+  write(argspec, stderr())
+  q();
+}
+
+
+lib.load.quiet <- function( package ) {
+   package <- as.character(substitute(package))
+   suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
+}
+lib.load.quiet(getopt)
+lib.load.quiet( gplots )
+lib.load.quiet( amap )
+lib.load.quiet( ctc )
+if ( any( c( 'flashClust', 'fastcluster' ) %in% installed.packages() ) ) {
+  if ( 'flashClust' %in% installed.packages() ) {
+    lib.load.quiet( flashClust )
+  } else {
+    if ( 'fastcluster' %in% installed.packages() ) {
+      lib.load.quiet( fastcluster )
+    }
+  }
+}
+
+
+spec <- matrix( c( "dataset",             "d", 1, "character",
+                   "reverse.rows",        "r", 2, "character",
+                   "image.format",        "i", 2, "character",
+                   "output.fname",        "o", 2, "character",
+                   "output.report.html",  "h", 2, "character",
+                   "output.report.dir",   "p", 2, "character",
+                   "output.treeview",     "t", 2, "character"
+                   ),
+                nc=4,
+                byrow=TRUE
+               )
+
+
+opt <- getopt( spec=spec )
+if ( is.null( opt$image.format ) ){
+  opt$image.format <- "png"
+} else {
+  if ( ! opt$image.format %in% c( "pdf", "png" ) ) stop( 'invalid image format specified\n' )
+}
+if ( is.null( opt$output.report.dir ) ) { opt$output.report.dir <- "report" }
+if ( is.null( opt$output.report.html ) ) {
+  if ( opt$image.format == "pdf" ) opt$output.report.html <- "report/heatmap.pdf"
+  if ( opt$image.format == "png" ) opt$output.report.html <- "report/index.html"
+}
+if ( is.null( opt$output.treeview ) ) {
+  opt$output.treeview <- FALSE
+} else {
+  if ( ! opt$output.treeview %in% c( "no", "yes" ) ) {
+    stop( "invalid input to output.treeview param", opt$output.treeview, "\n" )
+  }
+  ##  set to TRUE/FALSE
+  opt$output.treeview <- ( opt$output.treeview == "yes" )
+}
+if ( is.null( opt$reverse.rows ) ) {
+  opt$reverse.rows <- TRUE
+}  else {
+  if ( ! opt$reverse.rows %in% c( "no", "yes" ) ) {
+    stop( "invalid input to reverse.rows param", opt$reverse.rows, "\n" )
+  }
+
+  ##  set to TRUE/FALSE
+  opt$reverse.rows <- ( opt$reverse.rows == "yes" )
+}
+
+if ( ( opt$image.format == "png" ) || opt$output.treeview ) {
+  if ( !file.exists( opt$output.report.dir ) ){
+    dir.create(opt$output.report.dir, recursive=T)
+  }
+}
+
+
+data <- as.matrix( read.delim(opt$dataset, row.names=1, check.names=F ) )  ## should load the cl, treecl.res (or partcl.res) and data
+hr <- hclust( Dist( data, "euclidean" ) )
+row.ddr <- as.dendrogram( hr )
+if ( opt$reverse.rows ) row.ddr <- rev( row.ddr )
+hc <- hclust( Dist( t( data ), "euclidean" ) )
+col.ddr <- as.dendrogram( hc )
+hmcols<-colorRampPalette(c("blue","white","red"))(256)
+
+param.list <- list( x=data,
+                    Rowv=row.ddr,
+                    Colv=col.ddr,
+                    dendrogram="both",
+                    trace="none",
+                    col=hmcols,
+                    symbreaks=TRUE,
+                    scale="none",
+                    labRow="",
+                    labCol="",
+                    na.color='grey' ) #,
+                    ##key=FALSE )
+
+
+if ( opt$image.format == 'png' ) {
+  
+  png.fname <- file.path( opt$output.report.dir, "cluster.heatmap.png")
+  plot.dev <- png( png.fname,
+                   width=8.5,
+                   height=11,
+                   units='in',
+                   res=72 )
+} else {
+  pdf.fname <- opt$output.report.html
+  pdf( opt$output.report.html,
+       paper="letter" )
+}
+
+heatmap.retval <- do.call( "heatmap.2", param.list )
+dev.off()
+
+if ( opt$image.format == 'png' ) {
+  pngs = list.files(path=opt$output.report.dir, patt="png")
+  html.out <- paste( "<html>",
+                     paste( paste( paste( "<div><img src=\'", pngs, sep="" ), "\'/></div>", sep="" ), collapse=""),
+                     "</html>" )
+  cat( html.out, file=opt$output.report.html )
+}
+
+
+if ( opt$output.treeview ) {
+  treeview.fname.stem <- file.path( opt$output.report.dir, "cluster.heatmap")
+  
+  fnames <- character()
+  fname <- paste( treeview.fname.stem, ".gtr", sep="" )
+  r2gtr( hr, file=fname )
+  fnames <- c( fnames, fname )
+
+  fname <- paste( treeview.fname.stem, ".atr", sep="" )
+  r2atr( hc, file=fname )
+  fnames <- c( fnames, fname )
+
+  fname <- paste( treeview.fname.stem, ".cdt", sep="" )
+  r2cdt( hr, hc, data, file=fname )
+  fnames <- c( fnames, fname )
+
+  ## jtv file now
+  jtv.str <- '<DocumentConfig><UrlExtractor/><ArrayUrlExtractor/><Views><View type="Dendrogram" dock="1"><ColorExtractor contrast="2.0"><ColorSet zero="#FFFFFF" down="#0000FF"/></ColorExtractor><ArrayDrawer/><GlobalXMap current="Fill"><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></GlobalXMap><GlobalYMap current="Fill"><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></GlobalYMap><ZoomXMap><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></ZoomXMap><ZoomYMap><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></ZoomYMap><TextView><TextView face="Monospaced" size="14"><GeneSummary/></TextView><TextView face="Monospaced" size="14"><GeneSummary/></TextView><TextView face="Monospaced" size="14"><GeneSummary/></TextView><TextView face="Monospaced" size="14"><GeneSummary/></TextView></TextView><ArrayNameView face="Monospaced" size="14"><ArraySummary included="0"/></ArrayNameView><AtrSummary/><GtrSummary/></View></Views></DocumentConfig>'
+  fname <- paste( treeview.fname.stem, ".jtv", sep="" )
+  cat( jtv.str, file=fname )
+  fnames <- c( fnames, fname )
+
+  cmd <- paste( "tar -zcf", opt$output.fname, paste( "--directory=", opt$output.report.dir, sep="" ), paste( basename( fnames ), collapse=" " ) )
+  system( cmd )
+}
+
+