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1 #!/usr/bin/env Rscript
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2 # Extract k cluster assignment from consensus clustering result Script by Peter Waltman
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3 # Nov. 12, 2012
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4 # License under Creative Commons Attribution 3.0 Unported (CC BY 3.0)
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5 #
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6 ##usage, options and doc goes here
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7 argspec <- c("galaxy.extract.cons.clustering.from.result.R extracts a cluster assignment for a specified
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8 value of K from a specified consensus cluster result file.
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9
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10
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11 Usage:
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12 galaxy.extract.cons.cluster.from.result.R -r <results_file> -k <k_select>
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13 Optional:
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14 -o consensus class output file # tab-delimitted file format
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15 \n\n")
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16 args <- commandArgs(TRUE)
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17 if ( length( args ) == 1 && args =="--help") {
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18 write( argspec, stderr() )
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19 q();
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20 }
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21
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22 library(getopt)
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23
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24 spec <- matrix( c( "results.file", "r", 1, "character",
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25 "k.select", "k", 1, "integer",
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26 "cluster.class.out", "o", 2, "character",
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27 "output.select.rdata", "d", 2, "character"
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28 ),
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29 nc=4,
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30 byrow=T
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31 )
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32 opt <- getopt( spec=spec )
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33 if ( is.null( opt$output.select.rdata ) ) { opt$output.select.rdata <- "select.RData" }
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34 ##if ( is.null( opt$cluster.class.out) ) { opt$cluster.class.out <- "select.cls" }
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35
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36 load( opt$results.file )
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37 cons.matrices <- lapply( results[ 2:length(results) ], '[[', 'consensusMatrix' )
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38 cls <- lapply( results[ 2:length(results) ], '[[', 'consensusClass' )
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39 names( cons.matrices ) <- names( cls ) <- 2:length( results )
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40 save.image( '~/tmp/extract.dbg.rda' )
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41 ch.k.select <- as.character( opt$k.select )
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42 if ( ch.k.select %in% names( cls ) ) {
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43 ## get the consensusClass file that's associated with the k.select
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44 cl <- cls[[ ch.k.select ]]
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45
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46 if ( ! is.null( opt$cluster.class.out ) ) {
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47 cl <- cbind( names( cl ), as.integer(cl) )
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48 colnames( cl ) <- c( "ID", "class" )
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49 write.table( cl, opt$cluster.class.out, sep="\t", row.names=FALSE, quote=FALSE )
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50 } else if ( ! is.null( opt$output.select.rdata ) ) {
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51 ## re-order the samples to follow the cluster assignment
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52 treecl.res <- results[[ opt$k.select ]]$consensusTree
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53 select.result <- results[[ opt$k.select ]]
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54
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55 if ( length(cl) == ncol(data) ) {
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56 names( cl ) <- treecl.res$labels <- select.result$consensusTree$labels <- colnames(data)
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57 } else if ( length(cl) == nrow(data) ) {
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58 names( cl ) <- treecl.res$labels <- select.result$consensusTree$labels <- rownames(data)
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59 } else {
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60 stop( "Number of clustered elements not equal to either number of rows or columns of data matrix\n" )
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61 }
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62
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63 save( file=opt$output.select.rdata, treecl.res, cl, select.result, data )
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64 } else {
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65 stop( 'no valid output format specified\n' )
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66 }
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67 } else {
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68 out.string <- paste( "choice of k =", ch.k.select, "not available in this result file. Max k = ", max( as.numeric( names(cls) ) ), "\n" )
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69 cat( out.string, file=opt$cluster.class.out )
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70 }
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71
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