Mercurial > repos > peter-waltman > ucsc_cluster_tools2

comparison cluster.tools/hclust.R @ 8:a58527c632b7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author peter-waltman
date Mon, 11 Mar 2013 16:31:29 -0400
parents 0decf3fd54bc
children
comparison
equal deleted inserted replaced
7:2efa1a284546 8:a58527c632b7
37 byrow=TRUE 37 byrow=TRUE
38 ) 38 )
39 39
40 opt <- getopt( spec=spec ) 40 opt <- getopt( spec=spec )
41 41
42 data <- as.matrix( read.delim( opt$data.fname, header=T, row.names=1 , check.names=FALSE ) )
42 if ( is.null( opt$distance.metric ) ) { opt$distance.metric <- "euclidean" } 43 if ( is.null( opt$distance.metric ) ) { opt$distance.metric <- "euclidean" }
43 if ( is.null( opt$dist.obj ) ) { opt$dist.obj <- FALSE } 44 if ( is.null( opt$dist.obj ) ) { opt$dist.obj <- FALSE }
44 if ( is.null( opt$direction ) ) { opt$direction <- "cols" } 45 if ( is.null( opt$direction ) ) { opt$direction <- "cols" }
45 if ( is.null( opt$linkage ) ) { opt$linkage <- "average" } 46 if ( is.null( opt$linkage ) ) { opt$linkage <- "average" }
46 if ( is.null( opt$num.k ) ) { opt$num.k <- 10 }
47 if ( is.null( opt$output.name ) ) { opt$output.name <- "hclust.result.rda" } 47 if ( is.null( opt$output.name ) ) { opt$output.name <- "hclust.result.rda" }
48 if ( is.null( opt$num.k ) || ( opt$num.k == -1 )) {
49 if ( opt$direction == 'cols' ) {
50 opt$num.k <- 5
51 } else if ( opt$direction == 'rows' ) {
52 opt$num.k <- nrow( data ) / 30 ## we use an estimated average size of gene clusters to be 30
53 if ( opt$num.k > 1000 ) {
54 opt$num.k <- ( opt$num.k %/% 10 ) * 10
55 } else {
56 opt$num.k <- ( opt$num.k %/% 5 ) * 5
57 }
58 }
59 }
48 60
49 data <- as.matrix( read.delim( opt$data.fname, header=T, row.names=1 , check.names=FALSE ) )
50 if ( opt$direction == "cols" ) { 61 if ( opt$direction == "cols" ) {
51 ## need to transpose b/c both kmeans & pam cluster the rows 62 ## need to transpose b/c both kmeans & pam cluster the rows
52 ## this shouldn't have an effect upon a distance matrix 63 ## this shouldn't have an effect upon a distance matrix
53 data <- t( data ) 64 data <- t( data )
54 } 65 }