annotate scripts/RaceID_class.R @ 0:e01c989c7543 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
author iuc
date Sat, 03 Mar 2018 17:34:16 -0500
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e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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1 ## load required packages.
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2 require(tsne)
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3 require(pheatmap)
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4 require(MASS)
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5 require(cluster)
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6 require(mclust)
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7 require(flexmix)
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8 require(lattice)
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9 require(fpc)
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10 require(amap)
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11 require(RColorBrewer)
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12 require(locfit)
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13
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14 ## class definition
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15 SCseq <- setClass("SCseq", slots = c(expdata = "data.frame", ndata = "data.frame", fdata = "data.frame", distances = "matrix", tsne = "data.frame", kmeans = "list", background = "list", out = "list", cpart = "vector", fcol = "vector", filterpar = "list", clusterpar = "list", outlierpar ="list" ))
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16
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17 setValidity("SCseq",
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18 function(object) {
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19 msg <- NULL
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20 if ( ! is.data.frame(object@expdata) ){
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21 msg <- c(msg, "input data must be data.frame")
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22 }else if ( nrow(object@expdata) < 2 ){
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23 msg <- c(msg, "input data must have more than one row")
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24 }else if ( ncol(object@expdata) < 2 ){
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25 msg <- c(msg, "input data must have more than one column")
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26 }else if (sum( apply( is.na(object@expdata),1,sum ) ) > 0 ){
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27 msg <- c(msg, "NAs are not allowed in input data")
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28 }else if (sum( apply( object@expdata,1,min ) ) < 0 ){
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29 msg <- c(msg, "negative values are not allowed in input data")
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30 }
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31 if (is.null(msg)) TRUE
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32 else msg
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33 }
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34 )
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35
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36 setMethod("initialize",
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37 signature = "SCseq",
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38 definition = function(.Object, expdata ){
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39 .Object@expdata <- expdata
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40 .Object@ndata <- expdata
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41 .Object@fdata <- expdata
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42 validObject(.Object)
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43 return(.Object)
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44 }
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45 )
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46
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47 setGeneric("filterdata", function(object, mintotal=3000, minexpr=5, minnumber=1, maxexpr=500, downsample=FALSE, dsn=1, rseed=17000) standardGeneric("filterdata"))
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48
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49 setMethod("filterdata",
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50 signature = "SCseq",
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51 definition = function(object,mintotal,minexpr,minnumber,maxexpr,downsample,dsn,rseed) {
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52 if ( ! is.numeric(mintotal) ) stop( "mintotal has to be a positive number" ) else if ( mintotal <= 0 ) stop( "mintotal has to be a positive number" )
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53 if ( ! is.numeric(minexpr) ) stop( "minexpr has to be a non-negative number" ) else if ( minexpr < 0 ) stop( "minexpr has to be a non-negative number" )
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54 if ( ! is.numeric(minnumber) ) stop( "minnumber has to be a non-negative integer number" ) else if ( round(minnumber) != minnumber | minnumber < 0 ) stop( "minnumber has to be a non-negative integer number" )
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55 if ( ! ( is.numeric(downsample) | is.logical(downsample) ) ) stop( "downsample has to be logical (TRUE/FALSE)" )
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56 if ( ! is.numeric(dsn) ) stop( "dsn has to be a positive integer number" ) else if ( round(dsn) != dsn | dsn <= 0 ) stop( "dsn has to be a positive integer number" )
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57 object@filterpar <- list(mintotal=mintotal, minexpr=minexpr, minnumber=minnumber, maxexpr=maxexpr, downsample=downsample, dsn=dsn)
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58 object@ndata <- object@expdata[,apply(object@expdata,2,sum,na.rm=TRUE) >= mintotal]
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59 if ( downsample ){
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60 set.seed(rseed)
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61 object@ndata <- downsample(object@expdata,n=mintotal,dsn=dsn)
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62 }else{
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63 x <- object@ndata
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64 object@ndata <- as.data.frame( t(t(x)/apply(x,2,sum))*median(apply(x,2,sum,na.rm=TRUE)) + .1 )
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65 }
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66 x <- object@ndata
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67 object@fdata <- x[apply(x>=minexpr,1,sum,na.rm=TRUE) >= minnumber,]
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68 x <- object@fdata
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69 object@fdata <- x[apply(x,1,max,na.rm=TRUE) < maxexpr,]
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70 return(object)
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71 }
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72 )
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73
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74
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75 downsample <- function(x,n,dsn){
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76 x <- round( x[,apply(x,2,sum,na.rm=TRUE) >= n], 0)
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77 nn <- min( apply(x,2,sum) )
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78 for ( j in 1:dsn ){
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79 z <- data.frame(GENEID=rownames(x))
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80 rownames(z) <- rownames(x)
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81 initv <- rep(0,nrow(z))
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82 for ( i in 1:dim(x)[2] ){
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83 y <- aggregate(rep(1,nn),list(sample(rep(rownames(x),x[,i]),nn)),sum)
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84 na <- names(x)[i]
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85 names(y) <- c("GENEID",na)
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86 rownames(y) <- y$GENEID
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diff changeset
87 z[,na] <- initv
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
88 k <- intersect(rownames(z),y$GENEID)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
89 z[k,na] <- y[k,na]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
90 z[is.na(z[,na]),na] <- 0
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
91 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
92 rownames(z) <- as.vector(z$GENEID)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
93 ds <- if ( j == 1 ) z[,-1] else ds + z[,-1]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
94 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
95 ds <- ds/dsn + .1
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
96 return(ds)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
97 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
98
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iuc
parents:
diff changeset
99 dist.gen <- function(x,method="euclidean", ...) if ( method %in% c("spearman","pearson","kendall") ) as.dist( 1 - cor(t(x),method=method,...) ) else dist(x,method=method,...)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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100
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iuc
parents:
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101 dist.gen.pairs <- function(x,y,...) dist.gen(t(cbind(x,y)),...)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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102
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iuc
parents:
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103 clustfun <- function(x,clustnr=20,bootnr=50,metric="pearson",do.gap=TRUE,SE.method="Tibs2001SEmax",SE.factor=.25,B.gap=50,cln=0,rseed=17000)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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parents:
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104 {
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iuc
parents:
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105 if ( clustnr < 2) stop("Choose clustnr > 1")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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106 di <- dist.gen(t(x),method=metric)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
107 if ( do.gap | cln > 0 ){
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iuc
parents:
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108 gpr <- NULL
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
109 if ( do.gap ){
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iuc
parents:
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110 set.seed(rseed)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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111 gpr <- clusGap(as.matrix(di), FUN = kmeans, K.max = clustnr, B = B.gap)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
112 if ( cln == 0 ) cln <- maxSE(gpr$Tab[,3],gpr$Tab[,4],method=SE.method,SE.factor)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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113 }
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iuc
parents:
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114 if ( cln <= 1 ) {
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iuc
parents:
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115 clb <- list(result=list(partition=rep(1,dim(x)[2])),bootmean=1)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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116 names(clb$result$partition) <- names(x)
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iuc
parents:
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117 return(list(x=x,clb=clb,gpr=gpr,di=di))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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118 }
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iuc
parents:
diff changeset
119 clb <- clusterboot(di,B=bootnr,distances=FALSE,bootmethod="boot",clustermethod=KmeansCBI,krange=cln,scaling=FALSE,multipleboot=FALSE,bscompare=TRUE,seed=rseed)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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120 return(list(x=x,clb=clb,gpr=gpr,di=di))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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121 }
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iuc
parents:
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122 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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123
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iuc
parents:
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124 KmeansCBI <- function (data, krange, k = NULL, scaling = FALSE, runs = 1,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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125 criterion = "ch", method="euclidean",...)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
126 {
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
127 if (!is.null(k))
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iuc
parents:
diff changeset
128 krange <- k
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iuc
parents:
diff changeset
129 if (!identical(scaling, FALSE))
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iuc
parents:
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130 sdata <- scale(data, center = TRUE, scale = scaling)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
131 else sdata <- data
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iuc
parents:
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132 c1 <- Kmeansruns(sdata, krange, runs = runs, criterion = criterion, method = method,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
133 ...)
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iuc
parents:
diff changeset
134 partition <- c1$cluster
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
135 cl <- list()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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136 nc <- krange
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iuc
parents:
diff changeset
137 for (i in 1:nc) cl[[i]] <- partition == i
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
138 out <- list(result = c1, nc = nc, clusterlist = cl, partition = partition,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
139 clustermethod = "kmeans")
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iuc
parents:
diff changeset
140 out
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iuc
parents:
diff changeset
141 }
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iuc
parents:
diff changeset
142
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iuc
parents:
diff changeset
143 Kmeansruns <- function (data, krange = 2:10, criterion = "ch", iter.max = 100,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
144 runs = 100, scaledata = FALSE, alpha = 0.001, critout = FALSE,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
145 plot = FALSE, method="euclidean", ...)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
146 {
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
147 data <- as.matrix(data)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
148 if (criterion == "asw")
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iuc
parents:
diff changeset
149 sdata <- dist(data)
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iuc
parents:
diff changeset
150 if (scaledata)
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iuc
parents:
diff changeset
151 data <- scale(data)
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iuc
parents:
diff changeset
152 cluster1 <- 1 %in% krange
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iuc
parents:
diff changeset
153 crit <- numeric(max(krange))
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iuc
parents:
diff changeset
154 km <- list()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
155 for (k in krange) {
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iuc
parents:
diff changeset
156 if (k > 1) {
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iuc
parents:
diff changeset
157 minSS <- Inf
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
158 kmopt <- NULL
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
159 for (i in 1:runs) {
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iuc
parents:
diff changeset
160 options(show.error.messages = FALSE)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
161 repeat {
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
162 kmm <- try(Kmeans(data, k, iter.max = iter.max, method=method,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
163 ...))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
164 if (class(kmm) != "try-error")
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iuc
parents:
diff changeset
165 break
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
166 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
167 options(show.error.messages = TRUE)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
168 swss <- sum(kmm$withinss)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
169 if (swss < minSS) {
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iuc
parents:
diff changeset
170 kmopt <- kmm
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
171 minSS <- swss
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iuc
parents:
diff changeset
172 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
173 if (plot) {
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
174 par(ask = TRUE)
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iuc
parents:
diff changeset
175 pairs(data, col = kmm$cluster, main = swss)
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iuc
parents:
diff changeset
176 }
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iuc
parents:
diff changeset
177 }
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iuc
parents:
diff changeset
178 km[[k]] <- kmopt
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
179 crit[k] <- switch(criterion, asw = cluster.stats(sdata,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
180 km[[k]]$cluster)$avg.silwidth, ch = calinhara(data,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
181 km[[k]]$cluster))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
182 if (critout)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
183 cat(k, " clusters ", crit[k], "\n")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
184 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
185 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
186 if (cluster1)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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187 cluster1 <- dudahart2(data, km[[2]]$cluster, alpha = alpha)$cluster1
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
188 k.best <- which.max(crit)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
189 if (cluster1)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
190 k.best <- 1
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
191 km[[k.best]]$crit <- crit
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
192 km[[k.best]]$bestk <- k.best
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
193 out <- km[[k.best]]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
194 out
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iuc
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diff changeset
195 }
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iuc
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diff changeset
196
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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197 binompval <- function(p,N,n){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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198 pval <- pbinom(n,round(N,0),p,lower.tail=TRUE)
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199 pval[!is.na(pval) & pval > 0.5] <- 1-pval[!is.na(pval) & pval > 0.5]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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200 return(pval)
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iuc
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201 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
202
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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203 setGeneric("clustexp", function(object,clustnr=20,bootnr=50,metric="pearson",do.gap=TRUE,SE.method="Tibs2001SEmax",SE.factor=.25,B.gap=50,cln=0,rseed=17000) standardGeneric("clustexp"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
204
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iuc
parents:
diff changeset
205 setMethod("clustexp",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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206 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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207 definition = function(object,clustnr,bootnr,metric,do.gap,SE.method,SE.factor,B.gap,cln,rseed) {
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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208 if ( ! is.numeric(clustnr) ) stop("clustnr has to be a positive integer") else if ( round(clustnr) != clustnr | clustnr <= 0 ) stop("clustnr has to be a positive integer")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
209 if ( ! is.numeric(bootnr) ) stop("bootnr has to be a positive integer") else if ( round(bootnr) != bootnr | bootnr <= 0 ) stop("bootnr has to be a positive integer")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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210 if ( ! ( metric %in% c( "spearman","pearson","kendall","euclidean","maximum","manhattan","canberra","binary","minkowski") ) ) stop("metric has to be one of the following: spearman, pearson, kendall, euclidean, maximum, manhattan, canberra, binary, minkowski")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
211 if ( ! ( SE.method %in% c( "firstSEmax","Tibs2001SEmax","globalSEmax","firstmax","globalmax") ) ) stop("SE.method has to be one of the following: firstSEmax, Tibs2001SEmax, globalSEmax, firstmax, globalmax")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
212 if ( ! is.numeric(SE.factor) ) stop("SE.factor has to be a non-negative integer") else if ( SE.factor < 0 ) stop("SE.factor has to be a non-negative integer")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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213 if ( ! ( is.numeric(do.gap) | is.logical(do.gap) ) ) stop( "do.gap has to be logical (TRUE/FALSE)" )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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214 if ( ! is.numeric(B.gap) ) stop("B.gap has to be a positive integer") else if ( round(B.gap) != B.gap | B.gap <= 0 ) stop("B.gap has to be a positive integer")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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215 if ( ! is.numeric(cln) ) stop("cln has to be a non-negative integer") else if ( round(cln) != cln | cln < 0 ) stop("cln has to be a non-negative integer")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
216 if ( ! is.numeric(rseed) ) stop("rseed has to be numeric")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
217 if ( !do.gap & cln == 0 ) stop("cln has to be a positive integer or do.gap has to be TRUE")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
218 object@clusterpar <- list(clustnr=clustnr,bootnr=bootnr,metric=metric,do.gap=do.gap,SE.method=SE.method,SE.factor=SE.factor,B.gap=B.gap,cln=cln,rseed=rseed)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
219 y <- clustfun(object@fdata,clustnr,bootnr,metric,do.gap,SE.method,SE.factor,B.gap,cln,rseed)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
220 object@kmeans <- list(kpart=y$clb$result$partition, jaccard=y$clb$bootmean, gap=y$gpr)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
221 object@distances <- as.matrix( y$di )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
222 set.seed(111111)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
223 object@fcol <- sample(rainbow(max(y$clb$result$partition)))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
224 return(object)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
225 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
226 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
227
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
228 setGeneric("findoutliers", function(object,outminc=5,outlg=2,probthr=1e-3,thr=2**-(1:40),outdistquant=.75) standardGeneric("findoutliers"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
229
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
230 setMethod("findoutliers",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
231 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
232 definition = function(object,outminc,outlg,probthr,thr,outdistquant) {
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
233 if ( length(object@kmeans$kpart) == 0 ) stop("run clustexp before findoutliers")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
234 if ( ! is.numeric(outminc) ) stop("outminc has to be a non-negative integer") else if ( round(outminc) != outminc | outminc < 0 ) stop("outminc has to be a non-negative integer")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
235 if ( ! is.numeric(outlg) ) stop("outlg has to be a non-negative integer") else if ( round(outlg) != outlg | outlg < 0 ) stop("outlg has to be a non-negative integer")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
236 if ( ! is.numeric(probthr) ) stop("probthr has to be a number between 0 and 1") else if ( probthr < 0 | probthr > 1 ) stop("probthr has to be a number between 0 and 1")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
237 if ( ! is.numeric(thr) ) stop("thr hast to be a vector of numbers between 0 and 1") else if ( min(thr) < 0 | max(thr) > 1 ) stop("thr hast to be a vector of numbers between 0 and 1")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
238 if ( ! is.numeric(outdistquant) ) stop("outdistquant has to be a number between 0 and 1") else if ( outdistquant < 0 | outdistquant > 1 ) stop("outdistquant has to be a number between 0 and 1")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
239
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
240 object@outlierpar <- list( outminc=outminc,outlg=outlg,probthr=probthr,thr=thr,outdistquant=outdistquant )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
241 ### calibrate background model
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
242 m <- log2(apply(object@fdata,1,mean))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
243 v <- log2(apply(object@fdata,1,var))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
244 f <- m > -Inf & v > -Inf
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
245 m <- m[f]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
246 v <- v[f]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
247 mm <- -8
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
248 repeat{
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
249 fit <- lm(v ~ m + I(m^2))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
250 if( coef(fit)[3] >= 0 | mm >= 3){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
251 break
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
252 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
253 mm <- mm + .5
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
254 f <- m > mm
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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diff changeset
255 m <- m[f]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
256 v <- v[f]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
257 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
258 object@background <- list()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
259 object@background$vfit <- fit
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
260 object@background$lvar <- function(x,object) 2**(coef(object@background$vfit)[1] + log2(x)*coef(object@background$vfit)[2] + coef(object@background$vfit)[3] * log2(x)**2)
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261 object@background$lsize <- function(x,object) x**2/(max(x + 1e-6,object@background$lvar(x,object)) - x)
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262
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263 ### identify outliers
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264 out <- c()
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265 stest <- rep(0,length(thr))
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266 cprobs <- c()
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iuc
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267 for ( n in 1:max(object@kmeans$kpart) ){
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268 if ( sum(object@kmeans$kpart == n) == 1 ){ cprobs <- append(cprobs,.5); names(cprobs)[length(cprobs)] <- names(object@kmeans$kpart)[object@kmeans$kpart == n]; next }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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269 x <- object@fdata[,object@kmeans$kpart == n]
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270 x <- x[apply(x,1,max) > outminc,]
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271 z <- t( apply(x,1,function(x){ apply( cbind( pnbinom(round(x,0),mu=mean(x),size=object@background$lsize(mean(x),object)) , 1 - pnbinom(round(x,0),mu=mean(x),size=object@background$lsize(mean(x),object)) ),1, min) } ) )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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272 cp <- apply(z,2,function(x){ y <- p.adjust(x,method="BH"); y <- y[order(y,decreasing=FALSE)]; return(y[outlg]);})
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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273 f <- cp < probthr
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274 cprobs <- append(cprobs,cp)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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275 if ( sum(f) > 0 ) out <- append(out,names(x)[f])
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276 for ( j in 1:length(thr) ) stest[j] <- stest[j] + sum( cp < thr[j] )
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277 }
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278 object@out <-list(out=out,stest=stest,thr=thr,cprobs=cprobs)
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279
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280 ### cluster outliers
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281 clp2p.cl <- c()
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282 cols <- names(object@fdata)
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283 di <- as.data.frame(object@distances)
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iuc
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284 for ( i in 1:max(object@kmeans$kpart) ) {
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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285 tcol <- cols[object@kmeans$kpart == i]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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286 if ( sum(!(tcol %in% out)) > 1 ) clp2p.cl <- append(clp2p.cl,as.vector(t(di[tcol[!(tcol %in% out)],tcol[!(tcol %in% out)]])))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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287 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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288 clp2p.cl <- clp2p.cl[clp2p.cl>0]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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289
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290 cpart <- object@kmeans$kpart
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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291 cadd <- list()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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292 if ( length(out) > 0 ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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293 if (length(out) == 1){
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294 cadd <- list(out)
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295 }else{
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296 n <- out
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297 m <- as.data.frame(di[out,out])
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298
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299 for ( i in 1:length(out) ){
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300 if ( length(n) > 1 ){
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301 o <- order(apply(cbind(m,1:dim(m)[1]),1,function(x) min(x[1:(length(x)-1)][-x[length(x)]])),decreasing=FALSE)
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302 m <- m[o,o]
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303 n <- n[o]
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304 f <- m[,1] < quantile(clp2p.cl,outdistquant) | m[,1] == min(clp2p.cl)
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305 ind <- 1
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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306 if ( sum(f) > 1 ) for ( j in 2:sum(f) ) if ( apply(m[f,f][j,c(ind,j)] > quantile(clp2p.cl,outdistquant) ,1,sum) == 0 ) ind <- append(ind,j)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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307 cadd[[i]] <- n[f][ind]
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308 g <- ! n %in% n[f][ind]
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309 n <- n[g]
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310 m <- m[g,g]
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311 if ( sum(g) == 0 ) break
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312
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313 }else if (length(n) == 1){
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314 cadd[[i]] <- n
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parents:
diff changeset
315 break
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diff changeset
316 }
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317 }
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318 }
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319
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iuc
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320 for ( i in 1:length(cadd) ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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321 cpart[cols %in% cadd[[i]]] <- max(cpart) + 1
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322 }
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323 }
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324
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parents:
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325 ### determine final clusters
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iuc
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326 for ( i in 1:max(cpart) ){
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parents:
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327 d <- object@fdata[,cols[cpart == i]]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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328 if ( sum(cpart == i) == 1 ) cent <- d else cent <- apply(d,1,mean)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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parents:
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329 if ( i == 1 ) dcent <- data.frame(cent) else dcent <- cbind(dcent,cent)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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parents:
diff changeset
330 if ( i == 1 ) tmp <- data.frame(apply(object@fdata[,cols],2,dist.gen.pairs,y=cent,method=object@clusterpar$metric)) else tmp <- cbind(tmp,apply(object@fdata[,cols],2,dist.gen.pairs,y=cent,method=object@clusterpar$metric))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
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diff changeset
331 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
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332 cpart <- apply(tmp,1,function(x) order(x,decreasing=FALSE)[1])
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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333
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parents:
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334 for ( i in max(cpart):1){if (sum(cpart==i)==0) cpart[cpart>i] <- cpart[cpart>i] - 1 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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335
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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parents:
diff changeset
336 object@cpart <- cpart
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337
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338 set.seed(111111)
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339 object@fcol <- sample(rainbow(max(cpart)))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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parents:
diff changeset
340 return(object)
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341 }
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iuc
parents:
diff changeset
342 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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343
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344 setGeneric("plotgap", function(object) standardGeneric("plotgap"))
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345
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parents:
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346 setMethod("plotgap",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
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diff changeset
347 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
348 definition = function(object){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
349 if ( length(object@kmeans$kpart) == 0 ) stop("run clustexp before plotgap")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
350 plot(object@kmeans$gap)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
351 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
352 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
353
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
354 setGeneric("plotsilhouette", function(object) standardGeneric("plotsilhouette"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
355
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
356 setMethod("plotsilhouette",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
357 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
358 definition = function(object){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
359 if ( length(object@kmeans$kpart) == 0 ) stop("run clustexp before plotsilhouette")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
360 if ( length(unique(object@kmeans$kpart)) < 2 ) stop("only a single cluster: no silhouette plot")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
361 kpart <- object@kmeans$kpart
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
362 distances <- dist.gen(object@distances)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
363 si <- silhouette(kpart,distances)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
364 plot(si)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
365 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
366 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
367
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
368 setGeneric("plotjaccard", function(object) standardGeneric("plotjaccard"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
369
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
370 setMethod("plotjaccard",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
371 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
372 definition = function(object){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
373 if ( length(object@kmeans$kpart) == 0 ) stop("run clustexp before plotjaccard")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
374 if ( length(unique(object@kmeans$kpart)) < 2 ) stop("only a single cluster: no Jaccard's similarity plot")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
375 barplot(object@kmeans$jaccard,names.arg=1:length(object@kmeans$jaccard),ylab="Jaccard's similarity")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
376 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
377 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
378
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
379 setGeneric("plotoutlierprobs", function(object) standardGeneric("plotoutlierprobs"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
380
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
381 setMethod("plotoutlierprobs",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
382 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
383 definition = function(object){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
384 if ( length(object@cpart) == 0 ) stop("run findoutliers before plotoutlierprobs")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
385 p <- object@kmeans$kpart[ order(object@kmeans$kpart,decreasing=FALSE)]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
386 x <- object@out$cprobs[names(p)]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
387 fcol <- object@fcol
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
388 for ( i in 1:max(p) ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
389 y <- -log10(x + 2.2e-16)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
390 y[p != i] <- 0
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
391 if ( i == 1 ) b <- barplot(y,ylim=c(0,max(-log10(x + 2.2e-16))*1.1),col=fcol[i],border=fcol[i],names.arg=FALSE,ylab="-log10prob") else barplot(y,add=TRUE,col=fcol[i],border=fcol[i],names.arg=FALSE,axes=FALSE)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
392 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
393 abline(-log10(object@outlierpar$probthr),0,col="black",lty=2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
394 d <- b[2,1] - b[1,1]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
395 y <- 0
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
396 for ( i in 1:max(p) ) y <- append(y,b[sum(p <=i),1] + d/2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
397 axis(1,at=(y[1:(length(y)-1)] + y[-1])/2,lab=1:max(p))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
398 box()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
399 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
400 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
401
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
402 setGeneric("plotbackground", function(object) standardGeneric("plotbackground"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
403
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
404 setMethod("plotbackground",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
405 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
406 definition = function(object){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
407 if ( length(object@cpart) == 0 ) stop("run findoutliers before plotbackground")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
408 m <- apply(object@fdata,1,mean)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
409 v <- apply(object@fdata,1,var)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
410 fit <- locfit(v~lp(m,nn=.7),family="gamma",maxk=500)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
411 plot(log2(m),log2(v),pch=20,xlab="log2mean",ylab="log2var",col="grey")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
412 lines(log2(m[order(m)]),log2(object@background$lvar(m[order(m)],object)),col="red",lwd=2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
413 lines(log2(m[order(m)]),log2(fitted(fit)[order(m)]),col="orange",lwd=2,lty=2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
414 legend("topleft",legend=substitute(paste("y = ",a,"*x^2 + ",b,"*x + ",d,sep=""),list(a=round(coef(object@background$vfit)[3],2),b=round(coef(object@background$vfit)[2],2),d=round(coef(object@background$vfit)[1],2))),bty="n")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
415 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
416 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
417
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
418 setGeneric("plotsensitivity", function(object) standardGeneric("plotsensitivity"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
419
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
420 setMethod("plotsensitivity",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
421 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
422 definition = function(object){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
423 if ( length(object@cpart) == 0 ) stop("run findoutliers before plotsensitivity")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
424 plot(log10(object@out$thr), object@out$stest, type="l",xlab="log10 Probability cutoff", ylab="Number of outliers")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
425 abline(v=log10(object@outlierpar$probthr),col="red",lty=2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
426 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
427 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
428
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
429 setGeneric("clustdiffgenes", function(object,pvalue=.01) standardGeneric("clustdiffgenes"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
430
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
431 setMethod("clustdiffgenes",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
432 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
433 definition = function(object,pvalue){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
434 if ( length(object@cpart) == 0 ) stop("run findoutliers before clustdiffgenes")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
435 if ( ! is.numeric(pvalue) ) stop("pvalue has to be a number between 0 and 1") else if ( pvalue < 0 | pvalue > 1 ) stop("pvalue has to be a number between 0 and 1")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
436 cdiff <- list()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
437 x <- object@ndata
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
438 y <- object@expdata[,names(object@ndata)]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
439 part <- object@cpart
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
440 for ( i in 1:max(part) ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
441 if ( sum(part == i) == 0 ) next
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
442 m <- apply(x,1,mean)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
443 n <- if ( sum(part == i) > 1 ) apply(x[,part == i],1,mean) else x[,part == i]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
444 no <- if ( sum(part == i) > 1 ) median(apply(y[,part == i],2,sum))/median(apply(x[,part == i],2,sum)) else sum(y[,part == i])/sum(x[,part == i])
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
445 m <- m*no
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
446 n <- n*no
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
447 pv <- binompval(m/sum(m),sum(n),n)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
448 d <- data.frame(mean.all=m,mean.cl=n,fc=n/m,pv=pv)[order(pv,decreasing=FALSE),]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
449 cdiff[[paste("cl",i,sep=".")]] <- d[d$pv < pvalue,]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
450 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
451 return(cdiff)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
452 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
453 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
454
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
455 setGeneric("diffgenes", function(object,cl1,cl2,mincount=5) standardGeneric("diffgenes"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
456
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
457 setMethod("diffgenes",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
458 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
459 definition = function(object,cl1,cl2,mincount){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
460 part <- object@cpart
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
461 cl1 <- c(cl1)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
462 cl2 <- c(cl2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
463 if ( length(part) == 0 ) stop("run findoutliers before diffgenes")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
464 if ( ! is.numeric(mincount) ) stop("mincount has to be a non-negative number") else if ( mincount < 0 ) stop("mincount has to be a non-negative number")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
465 if ( length(intersect(cl1, part)) < length(unique(cl1)) ) stop( paste("cl1 has to be a subset of ",paste(sort(unique(part)),collapse=","),"\n",sep="") )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
466 if ( length(intersect(cl2, part)) < length(unique(cl2)) ) stop( paste("cl2 has to be a subset of ",paste(sort(unique(part)),collapse=","),"\n",sep="") )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
467 f <- apply(object@ndata[,part %in% c(cl1,cl2)],1,max) > mincount
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
468 x <- object@ndata[f,part %in% cl1]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
469 y <- object@ndata[f,part %in% cl2]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
470 if ( sum(part %in% cl1) == 1 ) m1 <- x else m1 <- apply(x,1,mean)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
471 if ( sum(part %in% cl2) == 1 ) m2 <- y else m2 <- apply(y,1,mean)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
472 if ( sum(part %in% cl1) == 1 ) s1 <- sqrt(x) else s1 <- sqrt(apply(x,1,var))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
473 if ( sum(part %in% cl2) == 1 ) s2 <- sqrt(y) else s2 <- sqrt(apply(y,1,var))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
474
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
475 d <- ( m1 - m2 )/ apply( cbind( s1, s2 ),1,mean )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
476 names(d) <- rownames(object@ndata)[f]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
477 if ( sum(part %in% cl1) == 1 ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
478 names(x) <- names(d)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
479 x <- x[order(d,decreasing=TRUE)]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
480 }else{
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
481 x <- x[order(d,decreasing=TRUE),]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
482 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
483 if ( sum(part %in% cl2) == 1 ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
484 names(y) <- names(d)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
485 y <- y[order(d,decreasing=TRUE)]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
486 }else{
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
487 y <- y[order(d,decreasing=TRUE),]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
488 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
489 return(list(z=d[order(d,decreasing=TRUE)],cl1=x,cl2=y,cl1n=cl1,cl2n=cl2))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
490 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
491 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
492
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
493 plotdiffgenes <- function(z,gene=g){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
494 if ( ! is.list(z) ) stop("first arguments needs to be output of function diffgenes")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
495 if ( length(z) < 5 ) stop("first arguments needs to be output of function diffgenes")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
496 if ( sum(names(z) == c("z","cl1","cl2","cl1n","cl2n")) < 5 ) stop("first arguments needs to be output of function diffgenes")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
497 if ( length(gene) > 1 ) stop("only single value allowed for argument gene")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
498 if ( !is.numeric(gene) & !(gene %in% names(z$z)) ) stop("argument gene needs to be within rownames of first argument or a positive integer number")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
499 if ( is.numeric(gene) ){ if ( gene < 0 | round(gene) != gene ) stop("argument gene needs to be within rownames of first argument or a positive integer number") }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
500 x <- if ( is.null(dim(z$cl1)) ) z$cl1[gene] else t(z$cl1[gene,])
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
501 y <- if ( is.null(dim(z$cl2)) ) z$cl2[gene] else t(z$cl2[gene,])
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
502 plot(1:length(c(x,y)),c(x,y),ylim=c(0,max(c(x,y))),xlab="",ylab="Expression",main=gene,cex=0,axes=FALSE)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
503 axis(2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
504 box()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
505 u <- 1:length(x)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
506 rect(u - .5,0,u + .5,x,col="red")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
507 v <- c(min(u) - .5,max(u) + .5)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
508 axis(1,at=mean(v),lab=paste(z$cl1n,collapse=","))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
509 lines(v,rep(mean(x),length(v)))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
510 lines(v,rep(mean(x)-sqrt(var(x)),length(v)),lty=2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
511 lines(v,rep(mean(x)+sqrt(var(x)),length(v)),lty=2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
512
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
513 u <- ( length(x) + 1 ):length(c(x,y))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
514 v <- c(min(u) - .5,max(u) + .5)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
515 rect(u - .5,0,u + .5,y,col="blue")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
516 axis(1,at=mean(v),lab=paste(z$cl2n,collapse=","))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
517 lines(v,rep(mean(y),length(v)))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
518 lines(v,rep(mean(y)-sqrt(var(y)),length(v)),lty=2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
519 lines(v,rep(mean(y)+sqrt(var(y)),length(v)),lty=2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
520 abline(v=length(x) + .5)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
521 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
522
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
523 setGeneric("clustheatmap", function(object,final=FALSE,hmethod="single") standardGeneric("clustheatmap"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
524
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
525 setMethod("clustheatmap",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
526 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
527 definition = function(object,final,hmethod){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
528 if ( final & length(object@cpart) == 0 ) stop("run findoutliers before clustheatmap")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
529 if ( !final & length(object@kmeans$kpart) == 0 ) stop("run clustexp before clustheatmap")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
530 x <- object@fdata
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
531 part <- if ( final ) object@cpart else object@kmeans$kpart
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
532 na <- c()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
533 j <- 0
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
534 for ( i in 1:max(part) ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
535 if ( sum(part == i) == 0 ) next
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
536 j <- j + 1
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
537 na <- append(na,i)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
538 d <- x[,part == i]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
539 if ( sum(part == i) == 1 ) cent <- d else cent <- apply(d,1,mean)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
540 if ( j == 1 ) tmp <- data.frame(cent) else tmp <- cbind(tmp,cent)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
541 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
542 names(tmp) <- paste("cl",na,sep=".")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
543 if ( max(part) > 1 ) cclmo <- hclust(dist.gen(as.matrix(dist.gen(t(tmp),method=object@clusterpar$metric))),method=hmethod)$order else cclmo <- 1
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
544 q <- part
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
545 for ( i in 1:max(part) ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
546 q[part == na[cclmo[i]]] <- i
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
547 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
548 part <- q
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
549 di <- as.data.frame( as.matrix( dist.gen(t(object@distances)) ) )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
550 pto <- part[order(part,decreasing=FALSE)]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
551 ptn <- c()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
552 for ( i in 1:max(pto) ){ pt <- names(pto)[pto == i]; z <- if ( length(pt) == 1 ) pt else pt[hclust(as.dist(t(di[pt,pt])),method=hmethod)$order]; ptn <- append(ptn,z) }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
553 col <- object@fcol
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
554 mi <- min(di,na.rm=TRUE)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
555 ma <- max(di,na.rm=TRUE)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
556 layout(matrix(data=c(1,3,2,4), nrow=2, ncol=2), widths=c(5,1,5,1), heights=c(5,1,1,1))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
557 ColorRamp <- colorRampPalette(brewer.pal(n = 7,name = "RdYlBu"))(100)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
558 ColorLevels <- seq(mi, ma, length=length(ColorRamp))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
559 if ( mi == ma ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
560 ColorLevels <- seq(0.99*mi, 1.01*ma, length=length(ColorRamp))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
561 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
562 par(mar = c(3,5,2.5,2))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
563 image(as.matrix(di[ptn,ptn]),col=ColorRamp,axes=FALSE)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
564 abline(0,1)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
565 box()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
566
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
567 tmp <- c()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
568 for ( u in 1:max(part) ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
569 ol <- (0:(length(part) - 1)/(length(part) - 1))[ptn %in% names(x)[part == u]]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
570 points(rep(0,length(ol)),ol,col=col[cclmo[u]],pch=15,cex=.75)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
571 points(ol,rep(0,length(ol)),col=col[cclmo[u]],pch=15,cex=.75)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
572 tmp <- append(tmp,mean(ol))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
573 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
574 axis(1,at=tmp,lab=cclmo)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
575 axis(2,at=tmp,lab=cclmo)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
576 par(mar = c(3,2.5,2.5,2))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
577 image(1, ColorLevels,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
578 matrix(data=ColorLevels, ncol=length(ColorLevels),nrow=1),
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
579 col=ColorRamp,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
580 xlab="",ylab="",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
581 xaxt="n")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
582 layout(1)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
583 return(cclmo)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
584 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
585 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
586
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
587 setGeneric("comptsne", function(object,rseed=15555) standardGeneric("comptsne"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
588
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
589 setMethod("comptsne",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
590 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
591 definition = function(object,rseed){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
592 if ( length(object@kmeans$kpart) == 0 ) stop("run clustexp before comptsne")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
593 set.seed(rseed)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
594 di <- dist.gen(as.matrix(object@distances))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
595 ts <- tsne(di,k=2)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
596 object@tsne <- as.data.frame(ts)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
597 return(object)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
598 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
599 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
600
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
601 setGeneric("plottsne", function(object,final=TRUE) standardGeneric("plottsne"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
602
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
603 setMethod("plottsne",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
604 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
605 definition = function(object,final){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
606 if ( length(object@tsne) == 0 ) stop("run comptsne before plottsne")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
607 if ( final & length(object@cpart) == 0 ) stop("run findoutliers before plottsne")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
608 if ( !final & length(object@kmeans$kpart) == 0 ) stop("run clustexp before plottsne")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
609 part <- if ( final ) object@cpart else object@kmeans$kpart
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
610 plot(object@tsne,xlab="Dim 1",ylab="Dim 2",pch=20,cex=1.5,col="lightgrey")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
611 for ( i in 1:max(part) ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
612 if ( sum(part == i) > 0 ) text(object@tsne[part == i,1],object@tsne[part == i,2],i,col=object@fcol[i],cex=.75,font=4)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
613 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
614 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
615 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
616
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
617 setGeneric("plotlabelstsne", function(object,labels=NULL) standardGeneric("plotlabelstsne"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
618
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
619 setMethod("plotlabelstsne",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
620 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
621 definition = function(object,labels){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
622 if ( is.null(labels ) ) labels <- names(object@ndata)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
623 if ( length(object@tsne) == 0 ) stop("run comptsne before plotlabelstsne")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
624 plot(object@tsne,xlab="Dim 1",ylab="Dim 2",pch=20,cex=1.5,col="lightgrey")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
625 text(object@tsne[,1],object@tsne[,2],labels,cex=.5)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
626 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
627 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
628
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
629 setGeneric("plotsymbolstsne", function(object,types=NULL) standardGeneric("plotsymbolstsne"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
630
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
631 setMethod("plotsymbolstsne",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
632 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
633 definition = function(object,types){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
634 if ( is.null(types) ) types <- names(object@fdata)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
635 if ( length(object@tsne) == 0 ) stop("run comptsne before plotsymbolstsne")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
636 if ( length(types) != ncol(object@fdata) ) stop("types argument has wrong length. Length has to equal to the column number of object@ndata")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
637 coloc <- rainbow(length(unique(types)))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
638 syms <- c()
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
639 plot(object@tsne,xlab="Dim 1",ylab="Dim 2",pch=20,col="grey")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
640 for ( i in 1:length(unique(types)) ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
641 f <- types == sort(unique(types))[i]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
642 syms <- append( syms, ( (i-1) %% 25 ) + 1 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
643 points(object@tsne[f,1],object@tsne[f,2],col=coloc[i],pch=( (i-1) %% 25 ) + 1,cex=1)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
644 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
645 legend("topleft", legend=sort(unique(types)), col=coloc, pch=syms)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
646 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
647 )
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
648
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
649 setGeneric("plotexptsne", function(object,g,n="",logsc=FALSE) standardGeneric("plotexptsne"))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
650
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
651 setMethod("plotexptsne",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
652 signature = "SCseq",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
653 definition = function(object,g,n="",logsc=FALSE){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
654 if ( length(object@tsne) == 0 ) stop("run comptsne before plottsne")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
655 if ( length(intersect(g,rownames(object@ndata))) < length(unique(g)) ) stop("second argument does not correspond to set of rownames slot ndata of SCseq object")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
656 if ( !is.numeric(logsc) & !is.logical(logsc) ) stop("argument logsc has to be logical (TRUE/FALSE)")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
657 if ( n == "" ) n <- g[1]
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
658 l <- apply(object@ndata[g,] - .1,2,sum) + .1
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
659 if (logsc) {
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
660 f <- l == 0
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
661 l <- log(l)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
662 l[f] <- NA
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
663 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
664 mi <- min(l,na.rm=TRUE)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
665 ma <- max(l,na.rm=TRUE)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
666 ColorRamp <- colorRampPalette(rev(brewer.pal(n = 7,name = "RdYlBu")))(100)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
667 ColorLevels <- seq(mi, ma, length=length(ColorRamp))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
668 v <- round((l - mi)/(ma - mi)*99 + 1,0)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
669 layout(matrix(data=c(1,3,2,4), nrow=2, ncol=2), widths=c(5,1,5,1), heights=c(5,1,1,1))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
670 par(mar = c(3,5,2.5,2))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
671 plot(object@tsne,xlab="Dim 1",ylab="Dim 2",main=n,pch=20,cex=0,col="grey")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
672 for ( k in 1:length(v) ){
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
673 points(object@tsne[k,1],object@tsne[k,2],col=ColorRamp[v[k]],pch=20,cex=1.5)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
674 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
675 par(mar = c(3,2.5,2.5,2))
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
676 image(1, ColorLevels,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
677 matrix(data=ColorLevels, ncol=length(ColorLevels),nrow=1),
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
678 col=ColorRamp,
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
679 xlab="",ylab="",
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
680 xaxt="n")
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
681 layout(1)
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
682 }
e01c989c7543 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid commit 39918bfdb08f06862ca395ce58a6f5e4f6dd1a5e
iuc
parents:
diff changeset
683 )