| Next changeset 1:08affc5d2aef (2015-10-09) |
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Commit message:
Imported from capsule None |
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added:
plot_from_lda.xml r_wrapper.sh test-data/lda_analy_output.txt test-data/plot_for_lda_output.pdf tool_dependencies.xml |
| b |
| diff -r 000000000000 -r c5ab37076128 plot_from_lda.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plot_from_lda.xml Mon Jul 28 11:56:27 2014 -0400 |
| [ |
| b'@@ -0,0 +1,262 @@\n+<tool id="plot_for_lda_output1" name="Draw ROC plot" version="1.0.1">\n+\t<description>on "Perform LDA" output</description>\n+ <requirements>\n+ <requirement type="package" version="2.11.0">R</requirement>\n+ </requirements>\n+\n+\t<command interpreter="sh">r_wrapper.sh $script_file</command>\n+\n+\t<inputs>\n+\t\t<param format="txt" name="input" type="data" label="Source file"> </param>\n+\t\t<param name="my_title" size="30" type="text" value="My Figure" label="Title of your plot" help="See syntax below"> </param>\n+\t\t<param name="X_axis" size="30" type="text" value="Text for X axis" label="Legend of X axis in your plot" help="See syntax below"> </param>\n+\t\t<param name="Y_axis" size="30" type="text" value="Text for Y axis" label="Legend of Y axis in your plot" help="See syntax below"> </param>\n+\t</inputs>\n+\t<outputs>\n+\t\t<data format="pdf" name="pdf_output" />\n+\t</outputs>\n+\n+\t<tests>\n+\t\t<test>\n+\t\t\t<param name="input" value="lda_analy_output.txt"/>\n+\t\t\t<param name="my_title" value="Test Plot1"/>\n+\t\t\t<param name="X_axis" value="Test Plot2"/>\n+\t\t\t<param name="Y_axis" value="Test Plot3"/>\n+\t\t\t<output name="pdf_output" file="plot_for_lda_output.pdf"/>\n+\t\t</test>\n+\t</tests>\n+\n+ <configfiles>\n+ <configfile name="script_file">\n+\n+ rm(list = objects() )\n+\n+ ############# FORMAT X DATA #########################\n+ format<-function(data) {\n+ ind=NULL\n+ for(i in 1 : ncol(data)){\n+ if (is.na(data[nrow(data),i])) {\n+ ind<-c(ind,i)\n+ }\n+ }\n+ #print(is.null(ind))\n+ if (!is.null(ind)) {\n+ data<-data[,-c(ind)]\n+ }\n+\n+ data\n+ }\n+\n+ ########GET RESPONSES ###############################\n+ get_resp<- function(data) {\n+ resp1<-as.vector(data[,ncol(data)])\n+ resp=numeric(length(resp1))\n+ for (i in 1:length(resp1)) {\n+ if (resp1[i]=="Control ") {\n+ resp[i] = 0\n+ }\n+ if (resp1[i]=="XLMR ") {\n+ resp[i] = 1\n+ }\n+ }\n+ return(resp)\n+ }\n+\n+ ######## CHARS TO NUMBERS ###########################\n+ f_to_numbers<- function(F) { \n+ ind<-NULL\n+ G<-matrix(0,nrow(F), ncol(F))\n+ for (i in 1:nrow(F)) {\n+ for (j in 1:ncol(F)) {\n+ G[i,j]<-as.integer(F[i,j])\n+ }\n+ }\n+ return(G)\n+ }\n+\n+ ###################NORMALIZING#########################\n+ norm <- function(M, a=NULL, b=NULL) {\n+ C<-NULL\n+ ind<-NULL\n+\n+ for (i in 1: ncol(M)) {\n+ if (sd(M[,i])!=0) {\n+ M[,i]<-(M[,i]-mean(M[,i]))/sd(M[,i])\n+ }\n+ # else {print(mean(M[,i]))} \n+ }\n+ return(M)\n+ }\n+\n+ ##### LDA DIRECTIONS #################################\n+ lda_dec <- function(data, k){\n+ priors=numeric(k)\n+ grandmean<-numeric(ncol(data)-1)\n+ means=matrix(0,k,ncol(data)-1)\n+ B = matrix(0, ncol(data)-1, ncol(data)-1)\n+ N=nrow(data)\n+ for (i in 1:k){\n+ priors[i]=sum(data[,1]==i)/N\n+ grp=subset(data,data\\$group==i)\n+ means[i,]=mean(grp[,2:ncol(data)])\n+ #print(means[i,])\n+ #print(priors[i])\n+ #print(priors[i]*means[i,])\n+ grandmean = priors[i]*means[i,] + grandmean \n+ }\n+\n+ for (i in 1:k) {\n+ B= B + priors[i]*((means[i,]-grandmean)%*%t(means[i,]-grandmean))\n+ }\n+ \n+ W = var(data[,2:ncol(data)])\n+ svdW = svd(W)\n+ inv_sqrtW =solve(svdW\\$v %*% diag(sqrt(svdW\\$d)) %*% t(svdW\\$v)'..b'+ }\n+ else {\n+ cl[1]=2 \n+ cl[2]=1\n+ }\n+\n+ for (i in 1:length(test_data)) {\n+\n+ if (test_data[i] <= cutoff) {\n+ predclass[i] = cl[1]\n+ }\n+ else {\n+ predclass[i] = cl[2] \n+ } \n+ }\n+ #print(means)\n+ #print(mean(means))\n+ #X11()\n+ #plot(test_data,pch=predclass, col=resp) \n+ predclass\n+ }\n+\n+ ################# EXTENDED ERROR RATES #################\n+ ext_error_rate <- function(predclass, actualclass,msg=c("you forgot the message"), pr=1) {\n+ er=sum(predclass != actualclass)/length(predclass)\n+\n+ matr<-data.frame(predclass=predclass,actualclass=actualclass)\n+ escapes = subset(matr, actualclass==1)\n+ subjects = subset(matr, actualclass==2) \n+ er_esc=sum(escapes\\$predclass != escapes\\$actualclass)/length(escapes\\$predclass) \n+ er_subj=sum(subjects\\$predclass != subjects\\$actualclass)/length(subjects\\$predclass) \n+\n+ if (pr==1) {\n+ # print(paste(c(msg, \'overall : \', (1-er)*100, "%."),collapse=" "))\n+ # print(paste(c(msg, \'within escapes : \', (1-er_esc)*100, "%."),collapse=" "))\n+ # print(paste(c(msg, \'within subjects: \', (1-er_subj)*100, "%."),collapse=" ")) \n+ }\n+ return(c((1-er)*100, (1-er_esc)*100, (1-er_subj)*100)) \n+ }\n+\n+ ## Main Function ##\n+\n+\tfiles_alias<-c("${my_title}")\n+\ttau=seq(0,1,by=0.005)\n+\tnfiles=1\n+\tf = c("${input}")\n+\n+\trez_ext<-list()\n+\tfor (i in 1:nfiles) {\n+\t\trez_ext[[i]]<-dget(paste(f[i], sep="",collapse=""))\n+\t}\n+\n+\ttau<-tau[1:(length(tau)-1)]\n+\tfor (i in 1:nfiles) {\n+\t\trez_ext[[i]]<-rez_ext[[i]][,1:(length(tau)-1)]\n+\t}\n+\n+\t######## OPTIMAIL TAU ###########################\n+\n+\t#rez_ext\n+\n+\trate<-c("Optimal tau","Tr total", "Tr Y", "Tr X")\n+\n+\tm_tr<-numeric(nfiles)\n+\tm_xp22<-numeric(nfiles)\n+\tm_x<-numeric(nfiles)\n+\n+\tfor (i in 1:nfiles) {\n+\t\tr<-rez_ext[[i]]\n+\t\t#tr\n+\t#\trate<-rbind(rate, c(files_alias[i]," "," "," ") )\n+\t\tmm<-which((r[3,])==max(r[3,]))\n+\n+\t\tm_tr[i]<-mm[1]\n+\t\trate<-rbind(rate,c(tau[m_tr[i]],r[,m_tr[i]]))\n+\t}\n+\tprint(rate)\n+\n+\tpdf(file= paste("${pdf_output}"))\n+\n+\tplot(rez_ext[[i]][2,]~rez_ext[[i]][3,], xlim=c(0,100), ylim=c(0,100), xlab="${X_axis} [1-FP(False Positive)]", ylab="${Y_axis} [1-FP(False Positive)]", type="l", lty=1, col="blue", xaxt=\'n\', yaxt=\'n\')\n+\tfor (i in 1:nfiles) {\n+\t\tlines(rez_ext[[i]][2,]~rez_ext[[i]][3,], xlab="${X_axis} [1-FP(False Positive)]", ylab="${Y_axis} [1-FP(False Positive)]", type="l", lty=1, col=i) \n+\t\t# pt=c(r,)\n+\t\tpoints(x=rez_ext[[i]][3,m_tr[i]],y=rez_ext[[i]][2,m_tr[i]], pch=16, col=i) \n+\t}\n+\n+\n+\ttitle(main="${my_title}", adj=0, cex.main=1.1)\n+\taxis(2, at=c(0,20,40,60,80,100), labels=c(\'0\',\'20\',\'40\',\'60\',\'80\',\'100%\'))\n+\taxis(1, at=c(0,20,40,60,80,100), labels=c(\'0\',\'20\',\'40\',\'60\',\'80\',\'100%\')) \n+\n+\t#leg=c("10 kb","50 kb","100 kb")\n+\t#legend("bottomleft",legend=leg , col=c(1,2,3), lty=c(1,1,1))\n+\n+\t#dev.off()\n+\n+\t\t</configfile>\n+\t</configfiles>\n+\n+\n+\t<help>\n+.. class:: infomark\n+\n+**What it does**\n+\n+This tool generates a Receiver Operating Characteristic (ROC) plot that shows LDA classification success rates for different values of the tuning parameter tau as Figure 3 in Carrel et al., 2006 (PMID: 17009873).\n+\n+*Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, et al. (2006) Genomic Environment Predicts Expression Patterns on the Human Inactive X Chromosome. PLoS Genet 2(9): e151. doi:10.1371/journal.pgen.0020151*\n+\n+-----\n+\n+.. class:: warningmark\n+\n+**Note**\n+\n+- Output from "Perform LDA" tool is used as input file for this tool.\n+\n+</help>\n+\n+\n+\n+</tool>\n' |
| b |
| diff -r 000000000000 -r c5ab37076128 r_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_wrapper.sh Mon Jul 28 11:56:27 2014 -0400 |
| b |
| @@ -0,0 +1,23 @@ +#!/bin/sh + +### Run R providing the R script in $1 as standard input and passing +### the remaining arguments on the command line + +# Function that writes a message to stderr and exits +fail() +{ + echo "$@" >&2 + exit 1 +} + +# Ensure R executable is found +which R > /dev/null || fail "'R' is required by this tool but was not found on path" + +# Extract first argument +infile=$1; shift + +# Ensure the file exists +test -f $infile || fail "R input file '$infile' does not exist" + +# Invoke R passing file named by first argument to stdin +R --vanilla --slave $* < $infile |
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| diff -r 000000000000 -r c5ab37076128 test-data/lda_analy_output.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lda_analy_output.txt Mon Jul 28 11:56:27 2014 -0400 |
| b |
| b'@@ -0,0 +1,134 @@\n+structure(c(37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, \n+23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, 62.5, \n+37.9310344827586, 23.6363636363636, 62.5, 37.9310344827586, 23.6363636363636, \n+62.5, 37.9310344827586, 23.6363636363636, 62.5, 39.0804597701149, \n+23.6363636363636, 65.625, 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\n+23.6363636363636, 68.75, 40.2298850574713, 23.6363636363636, \n+68.75, 40.2298850574713, 23.636'..b'1.8181818181818, 78.125, 42.5287356321839, 21.8181818181818, \n+78.125, 42.5287356321839, 21.8181818181818, 78.125, 42.5287356321839, \n+21.8181818181818, 78.125, 42.5287356321839, 21.8181818181818, \n+78.125, 42.5287356321839, 21.8181818181818, 78.125, 42.5287356321839, \n+21.8181818181818, 78.125, 43.6781609195402, 21.8181818181818, \n+81.25, 43.6781609195402, 21.8181818181818, 81.25, 43.6781609195402, \n+21.8181818181818, 81.25, 43.6781609195402, 21.8181818181818, \n+81.25, 43.6781609195402, 21.8181818181818, 81.25, 43.6781609195402, \n+21.8181818181818, 81.25, 43.6781609195402, 21.8181818181818, \n+81.25, 43.6781609195402, 21.8181818181818, 81.25, 43.6781609195402, \n+21.8181818181818, 81.25, 43.6781609195402, 21.8181818181818, \n+81.25, 43.6781609195402, 21.8181818181818, 81.25, 43.6781609195402, \n+21.8181818181818, 81.25, 43.6781609195402, 21.8181818181818, \n+81.25, 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43.6781609195402, 21.8181818181818, 81.25, 43.6781609195402, \n+21.8181818181818, 81.25, 43.6781609195402, 21.8181818181818, \n+81.25, 56.3218390804598, 78.1818181818182, 18.75), .Dim = c(3L, \n+201L))\n' |
| b |
| diff -r 000000000000 -r c5ab37076128 test-data/plot_for_lda_output.pdf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plot_for_lda_output.pdf Mon Jul 28 11:56:27 2014 -0400 |
| [ |
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| diff -r 000000000000 -r c5ab37076128 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Jul 28 11:56:27 2014 -0400 |
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