Mercurial > repos > devteam > lda_analysis
changeset 0:f38763b52f33 draft
Imported from capsule None
| author | devteam |
|---|---|
| date | Mon, 28 Jul 2014 11:56:39 -0400 |
| parents | |
| children | f0b6217f4a0c |
| files | lda_analy.xml r_wrapper.sh test-data/lda_analy_output.txt test-data/matrix_generator_for_pc_and_lda_output.tabular tool_dependencies.xml |
| diffstat | 5 files changed, 539 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lda_analy.xml Mon Jul 28 11:56:39 2014 -0400 @@ -0,0 +1,288 @@ +<tool id="lda_analy1" name="Perform LDA" version="1.0.1"> + <description>Linear Discriminant Analysis</description> + <requirements> + <requirement type="package" version="2.11.0">R</requirement> + </requirements> + <command interpreter="sh">r_wrapper.sh $script_file</command> + <inputs> + <param format="tabular" name="input" type="data" label="Source file"/> + <param name="cond" size="30" type="integer" value="3" label="Number of principal components" help="See TIP below"> + <validator type="empty_field" message="Enter a valid number of principal components, see syntax below for examples"/> + </param> + + </inputs> + <outputs> + <data format="txt" name="output" /> + </outputs> + + <tests> + <test> + <param name="input" value="matrix_generator_for_pc_and_lda_output.tabular"/> + <output name="output" file="lda_analy_output.txt"/> + <param name="cond" value="2"/> + + </test> + </tests> + + <configfiles> + <configfile name="script_file"> + + rm(list = objects() ) + + ############# FORMAT X DATA ######################### + format<-function(data) { + ind=NULL + for(i in 1 : ncol(data)){ + if (is.na(data[nrow(data),i])) { + ind<-c(ind,i) + } + } + #print(is.null(ind)) + if (!is.null(ind)) { + data<-data[,-c(ind)] + } + + data + } + + ########GET RESPONSES ############################### + get_resp<- function(data) { + resp1<-as.vector(data[,ncol(data)]) + resp=numeric(length(resp1)) + for (i in 1:length(resp1)) { + if (resp1[i]=="Y ") { + resp[i] = 0 + } + if (resp1[i]=="X ") { + resp[i] = 1 + } + } + return(resp) + } + + ######## CHARS TO NUMBERS ########################### + f_to_numbers<- function(F) { + ind<-NULL + G<-matrix(0,nrow(F), ncol(F)) + for (i in 1:nrow(F)) { + for (j in 1:ncol(F)) { + G[i,j]<-as.integer(F[i,j]) + } + } + return(G) + } + + ###################NORMALIZING######################### + norm <- function(M, a=NULL, b=NULL) { + C<-NULL + ind<-NULL + + for (i in 1: ncol(M)) { + if (sd(M[,i])!=0) { + M[,i]<-(M[,i]-mean(M[,i]))/sd(M[,i]) + } + # else {print(mean(M[,i]))} + } + return(M) + } + + ##### LDA DIRECTIONS ################################# + lda_dec <- function(data, k){ + priors=numeric(k) + grandmean<-numeric(ncol(data)-1) + means=matrix(0,k,ncol(data)-1) + B = matrix(0, ncol(data)-1, ncol(data)-1) + N=nrow(data) + for (i in 1:k){ + priors[i]=sum(data[,1]==i)/N + grp=subset(data,data\$group==i) + means[i,]=mean(grp[,2:ncol(data)]) + #print(means[i,]) + #print(priors[i]) + #print(priors[i]*means[i,]) + grandmean = priors[i]*means[i,] + grandmean + } + + for (i in 1:k) { + B= B + priors[i]*((means[i,]-grandmean)%*%t(means[i,]-grandmean)) + } + + W = var(data[,2:ncol(data)]) + svdW = svd(W) + inv_sqrtW =solve(svdW\$v %*% diag(sqrt(svdW\$d)) %*% t(svdW\$v)) + B_star= t(inv_sqrtW)%*%B%*%inv_sqrtW + B_star_decomp = svd(B_star) + directions = inv_sqrtW%*%B_star_decomp\$v + return( list(directions, B_star_decomp\$d) ) + } + + ################ NAIVE BAYES FOR 1D SIR OR LDA ############## + naive_bayes_classifier <- function(resp, tr_data, test_data, k=2, tau) { + tr_data=data.frame(resp=resp, dir=tr_data) + means=numeric(k) + #print(k) + cl=numeric(k) + predclass=numeric(length(test_data)) + for (i in 1:k) { + grp = subset(tr_data, resp==i) + means[i] = mean(grp\$dir) + #print(i, means[i]) + } + cutoff = tau*means[1]+(1-tau)*means[2] + #print(tau) + #print(means) + #print(cutoff) + if (cutoff>means[1]) { + cl[1]=1 + cl[2]=2 + } + else { + cl[1]=2 + cl[2]=1 + } + + for (i in 1:length(test_data)) { + + if (test_data[i] <= cutoff) { + predclass[i] = cl[1] + } + else { + predclass[i] = cl[2] + } + } + #print(means) + #print(mean(means)) + #X11() + #plot(test_data,pch=predclass, col=resp) + predclass + } + + ################# EXTENDED ERROR RATES ################# + ext_error_rate <- function(predclass, actualclass,msg=c("you forgot the message"), pr=1) { + er=sum(predclass != actualclass)/length(predclass) + + matr<-data.frame(predclass=predclass,actualclass=actualclass) + escapes = subset(matr, actualclass==1) + subjects = subset(matr, actualclass==2) + er_esc=sum(escapes\$predclass != escapes\$actualclass)/length(escapes\$predclass) + er_subj=sum(subjects\$predclass != subjects\$actualclass)/length(subjects\$predclass) + + if (pr==1) { + # print(paste(c(msg, 'overall : ', (1-er)*100, "%."),collapse=" ")) + # print(paste(c(msg, 'within escapes : ', (1-er_esc)*100, "%."),collapse=" ")) + # print(paste(c(msg, 'within subjects: ', (1-er_subj)*100, "%."),collapse=" ")) + } + return(c((1-er)*100, (1-er_esc)*100, (1-er_subj)*100)) + } + + ## Main Function ## + + files<-matrix("${input}", 1,1, byrow=T) + + d<-"${cond}" # Number of PC + + tau<-seq(0,1, by=0.005) + #tau<-seq(0,1, by=0.1) + for_curve=matrix(-10, 3,length(tau)) + + ############################################################## + + test_data_whole_X <-read.delim(files[1,1], row.names=1) + + #### FORMAT TRAINING DATA #################################### + # get only necessary columns + + test_data_whole_X<-format(test_data_whole_X) + oligo_labels<-test_data_whole_X[1:(nrow(test_data_whole_X)-1),ncol(test_data_whole_X)] + test_data_whole_X<-test_data_whole_X[,1:(ncol(test_data_whole_X)-1)] + + X_names<-colnames(test_data_whole_X)[1:ncol(test_data_whole_X)] + test_data_whole_X<-t(test_data_whole_X) + resp<-get_resp(test_data_whole_X) + ldaqda_resp = resp + 1 + a<-sum(resp) # Number of Subject + b<-length(resp) - a # Number of Escape + ## FREQUENCIES ################################################# + F<-test_data_whole_X[,1:(ncol(test_data_whole_X)-1)] + F<-f_to_numbers(F) + FN<-norm(F, a, b) + ss<-svd(FN) + eigvar<-NULL + eig<-ss\$d^2 + + for ( i in 1:length(ss\$d)) { + eigvar[i]<-sum(eig[1:i])/sum(eig) + } + + #print(paste(c("Variance explained : ", eigvar[d]*100, "%"), collapse="")) + + Z<-F%*%ss\$v + + ldaqda_data <- data.frame(group=ldaqda_resp,Z[,1:d]) + lda_dir<-lda_dec(ldaqda_data,2) + train_lda_pred <-Z[,1:d]%*%lda_dir[[1]] + + ############# NAIVE BAYES CROSS-VALIDATION ############# + ### LDA ##### + + y<-ldaqda_resp + X<-F + cv<-matrix(c(rep('NA',nrow(test_data_whole_X))), nrow(test_data_whole_X), length(tau)) + for (i in 1:nrow(test_data_whole_X)) { + # print(i) + resp<-y[-i] + p<-matrix(X[-i,], dim(X)[1]-1, dim(X)[2]) + testdata<-matrix(X[i,],1,dim(X)[2]) + p1<-norm(p) + sss<-svd(p1) + pred<-(p%*%sss\$v)[,1:d] + test<- (testdata%*%sss\$v)[,1:d] + lda <- lda_dec(data.frame(group=resp,pred),2) + pred <- pred[,1:d]%*%lda[[1]][,1] + test <- test%*%lda[[1]][,1] + test<-matrix(test, 1, length(test)) + for (t in 1:length(tau)) { + cv[i, t] <- naive_bayes_classifier (resp, pred, test,k=2, tau[t]) + } + } + + for (t in 1:length(tau)) { + tr_err<-ext_error_rate(cv[,t], ldaqda_resp , c("CV"), 1) + for_curve[1:3,t]<-tr_err + } + + dput(for_curve, file="${output}") + + + </configfile> + </configfiles> + + <help> + +.. class:: infomark + +**TIP:** If you want to perform Principal Component Analysis (PCA) on the give numeric input data (which corresponds to the "Source file First in "Generate A Matrix" tool), please use *Multivariate Analysis/Principal Component Analysis* + +----- + +.. class:: infomark + +**What it does** + +This tool consists of the module to perform the Linear Discriminant Analysis as described in Carrel et al., 2006 (PMID: 17009873) + +*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* + +----- + +.. class:: warningmark + +**Note** + +- Output from "Generate A Matrix" tool is used as input file for this tool +- Output of this tool contains LDA classification success rates for different values of the turning parameter tau (from 0 to 1 with 0.005 interval). This output file will be used to establish the ROC plot, and you can obtain more detail information from this plot. + + +</help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/r_wrapper.sh Mon Jul 28 11:56:39 2014 -0400 @@ -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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