Mercurial > repos > peter-waltman > ucsc_cluster_tools2

comparison cluster.tools/heatmap.from.cluster.result.R @ 3:563832f48c08 draft

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author peter-waltman
date Fri, 01 Mar 2013 19:51:25 -0500
parents 0decf3fd54bc
children
comparison
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2:b8f262149ee2 3:563832f48c08
44 "survival.script", "z", 2, "character", 44 "survival.script", "z", 2, "character",
45 "cluster.fname", "C", 2, "character", 45 "cluster.fname", "C", 2, "character",
46 "survival.fname", "S", 2, "character", 46 "survival.fname", "S", 2, "character",
47 "survival.image", "I", 2, "character", 47 "survival.image", "I", 2, "character",
48 "survival.mode", "M", 2, "character", 48 "survival.mode", "M", 2, "character",
49 "title", "T", 2, "character" 49 "survival.title", "T", 2, "character"
50 ), 50 ),
51 nc=4, 51 nc=4,
52 byrow=TRUE 52 byrow=TRUE
53 ) 53 )
54 54
330 330
331 ## get the consensusClass file that's associated with the k.select 331 ## get the consensusClass file that's associated with the k.select
332 cmd.string <- paste( cmd.string, "-C", opt$dataset ) 332 cmd.string <- paste( cmd.string, "-C", opt$dataset )
333 cmd.string <- paste( cmd.string, "-S", opt$survival.fname ) 333 cmd.string <- paste( cmd.string, "-S", opt$survival.fname )
334 cmd.string <- paste( cmd.string, "-M", opt$survival.mode ) 334 cmd.string <- paste( cmd.string, "-M", opt$survival.mode )
335 if ( ! is.null( opt$suvival.title ) )
336 cmd.string <- paste( cmd.string, "-T", opt$suvival.title )
335 337
336 ## only call kms if we're the image is png 338 ## only call kms if we're the image is png
337 if ( opt$image.format=="png" ) { 339 if ( opt$image.format=="png" ) {
338 png.fname <- file.path( opt$output.report.dir, "kaplan.meier.survival.png") 340 png.fname <- file.path( opt$output.report.dir, "kaplan.meier.survival.png")
339 cmd.string <- paste( cmd.string, "-I", "png" ) 341 cmd.string <- paste( cmd.string, "-I", "png" )