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1 #!/usr/bin/env Rscript
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2 argspec <- c("tab.2.cdt.R converts a data matrix to cdt format
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3
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4 Usage:
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5 tab.2.cdt.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 lib.load.quiet <- function( package ) {
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16 package <- as.character(substitute(package))
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17 suppressPackageStartupMessages( do.call( "library", list( package=package ) ) )
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18 }
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19
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20 lib.load.quiet( getopt )
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21 lib.load.quiet( ctc )
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22 if ( any( c( 'flashClust', 'fastcluster' ) %in% installed.packages() ) ) {
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23 if ( 'flashClust' %in% installed.packages() ) {
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24 lib.load.quiet( flashClust )
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25 } else {
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26 if ( 'fastcluster' %in% installed.packages() ) {
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27 lib.load.quiet( fastcluster )
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28 }
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29 }
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30 }
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31
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32 spec <- matrix( c( "dataset", "d", 1, "character",
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33 "num.k", "k", 1, "integer",
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34 "output.fname", "o", 2, "character"
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35 ),
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36 nc=4,
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37 byrow=TRUE
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38 )
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39
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40
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41 opt <- getopt( spec=spec )
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42 if ( is.null( opt$output.fname ) ) { opt$output.fname <- file.path( opt$output.report.dir, paste( "data", opt$output.format, sep="." ) ) }
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43
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44
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45 load( opt$dataset ) ## should load the cl, treecl.res (or partcl.res) and data
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46 if ( exists( 'treecl.res' ) ) {
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47 cutree.res <- cutree( treecl.res, k=opt$num.k )
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48 cl <- cutree.res
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49 save( file=opt$output.fname, treecl.res, cl, data )
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50 } else {
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51 stop( "no hierarchical clustering result found!\n" )
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52 }
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