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hartman-server/workflow/apps/r/joinInteractExps.R

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#!/usr/bin/env Rscript
# JoinInteractExps.R
library(plyr)
library(sos)
library(dplyr)
args <- commandArgs(TRUE)
# Set output dir
if (length(args) > 1) {
outDir <- args[1]
} else {
outDir <- "./" # for legacy workflow
}
# Set sd value
if (length(args) > 2) {
sd <- args[2]
} else {
sd <- 2 # default value
}
print(paste("SD=",sd))
# Set studyInfo file
if (length(args) > 3) {
studyInfo <- args[3]
} else {
studyInfo <- "../Code/StudyInfo.csv" # for legacy workflow
}
studies <- args[3:length(args)]
inputFiles <- c()
for (study in 1:length(studies)) {
zsFile <- file.path(study, 'zscores', 'zscores_interaction.csv')
if (file.exists(zsFile)) {
inputFiles[study] <- zsFile
}
}
print(length(inputFiles))
# TODO this is better handled in a loop in case you want to compare more experiments?
# The input is already designed for this
# Read in the files for your experiment and
# Join the two files at a time as a function of how many inputFile, list the larger file first ? in this example X2 has the larger number of genes.
# If X1 has a larger number of genes, switch the order of X1 and X2
if(length(inputFiles)==2) {
X1 <- read.csv(file=inputFiles[1],stringsAsFactors=FALSE)
X2 <- read.csv(file=inputFiles[2],stringsAsFactors=FALSE)
X <- join(X1,X2,by="OrfRep")
OBH=X[,order(colnames(X))] #OrderByHeader
headSel=select(OBH, contains('OrfRep'), matches('Gene'), contains('Z_lm_K'), contains('Z_Shift_K'),contains('Z_lm_L'), contains('Z_Shift_L'))
headSel=select(headSel, -'Gene.1') #remove 'Gene.1 column
headSel2=select(OBH, contains('OrfRep'), matches('Gene')) #Frame for interleaving Z_lm with Shift colums
headSel2=select(headSel2, -'Gene.1') #remove 'Gene.1 column #Frame for interleaving Z_lm with Shift colums
}else if(length(inputFiles)==3){
X1 <- read.csv(file=inputFiles[1],stringsAsFactors=FALSE) #exp1File,stringsAsFactors=FALSE)
X2 <- read.csv(file=inputFiles[2],stringsAsFactors=FALSE) #exp2File,stringsAsFactors=FALSE)
X3 <- read.csv(file=inputFiles[3],stringsAsFactors=FALSE) #exp3File,stringsAsFactors=FALSE)
X <- join(X1,X2,by="OrfRep")
X <- join(X,X3,by="OrfRep")
OBH=X[,order(colnames(X))] #OrderByHeader
headSel=select(OBH, contains('OrfRep'), matches('Gene'), contains('Z_lm_K'), contains('Z_Shift_K'),contains('Z_lm_L'), contains('Z_Shift_L'))
headSel=select(headSel, -'Gene.1',-'Gene.2')
headSel2=select(OBH, contains('OrfRep'), matches('Gene'))
headSel2=select(headSel2, -'Gene.1',-'Gene.2')
}else if(length(inputFiles)==4){
X1 <- read.csv(file=inputFiles[1],stringsAsFactors=FALSE) #exp1File,stringsAsFactors=FALSE)
X2 <- read.csv(file=inputFiles[2],stringsAsFactors=FALSE) #exp2File,stringsAsFactors=FALSE)
X3 <- read.csv(file=inputFiles[3],stringsAsFactors=FALSE) #exp3File,stringsAsFactors=FALSE)
X4 <- read.csv(file=inputFiles[4],stringsAsFactors=FALSE) #exp4File,stringsAsFactors=FALSE)
X <- join(X1,X2,by="OrfRep")
X <- join(X,X3,by="OrfRep")
X <- join(X,X4,by="OrfRep")
OBH=X[,order(colnames(X))] #OrderByHeader
headSel=select(OBH, contains('OrfRep'), matches('Gene'), contains('Z_lm_K'), contains('Z_Shift_K'),contains('Z_lm_L'), contains('Z_Shift_L'))
headSel=select(headSel, -'Gene.1',-'Gene.2',-'Gene.3')
headSel2=select(OBH, contains('OrfRep'), matches('Gene'))
headSel2=select(headSel2, -'Gene.1',-'Gene.2',-'Gene.3')
}
#headSel$contains('Z_Shift') %>% replace_na(0.001)
headers<-colnames(headSel)
i=0
for(i in 1:length(headers)){
if(grepl("Shift",headers[i])) {
headSel[headers[i]][is.na(headSel[headers[i]])]=0.001
}
if(grepl("Z_lm_",headers[i])) {
headSel[headers[i]][is.na(headSel[headers[i]])]=0.0001
}
}
#2SD option code to exclude Z_lm values less than 2 standard Deviations
REMcRdy=select(headSel, contains('OrfRep'), matches('Gene'), contains('Z_lm_'))
shiftOnly=select(headSel, contains('OrfRep'), matches('Gene'), contains('Z_Shift'))
# Code to replace the numeric (.1 .2 .3) headers with experiment names from StudyInfo.txt
Labels <- read.csv(file="../Code/StudyInfo.csv",stringsAsFactors=FALSE,sep=",")
# Using Text search grepl to relabel headers
REMcRdyHdr=colnames(REMcRdy)
REMcRdyLabels='asdf'
shftHdr=colnames(shiftOnly)
shiftLabels='asdf'
shiftLabels[1:2]<-shftHdr[1:2]
REMcRdyLabels[1:2]<-REMcRdyHdr[1:2]
for(i in 3:(length(shftHdr))){
if(i==3){
shiftLabels[3]<-paste0(Labels[1,2],".",shftHdr[3])
REMcRdyLabels[3]<-paste0(Labels[1,2],".",REMcRdyHdr[3]) }
if(i==5){
shiftLabels[5]<-paste0(Labels[1,2],".",shftHdr[5])
REMcRdyLabels[5]<-paste0(Labels[1,2],".",REMcRdyHdr[5])
}
if(i==7){
shiftLabels[7]<-paste0(Labels[1,2],".",shftHdr[7])
REMcRdyLabels[7]<-paste0(Labels[1,2],".",REMcRdyHdr[7])
}
if(grepl(".1",shftHdr[i],fixed=true)){
shiftLabels[i]<-paste0(Labels[2,2],".",shftHdr[i])
REMcRdyLabels[i]<-paste0(Labels[2,2],".",REMcRdyHdr[i])}
if (grepl(".2",shftHdr[i],fixed=true)){
shiftLabels[i]<-paste0(Labels[3,2],".",shftHdr[i])
REMcRdyLabels[i]<-paste0(Labels[3,2],".",REMcRdyHdr[i])}
if(grepl(".3",shftHdr[i],fixed=true)){
shiftLabels[i]<-paste0(Labels[4,2],".",shftHdr[i])
REMcRdyLabels[i]<-paste0(Labels[4,2],".",REMcRdyHdr[i])}
}
for(i in 3:(length(REMcRdyLabels))){
j=as.integer(i)
REMcRdyLabels[j]<- gsub("[.]", "_", REMcRdyLabels[j])
shiftLabels[j]<- gsub("[.]", "_", shiftLabels[j])
}
colnames(shiftOnly)<- shiftLabels
colnames(REMcRdy)<- REMcRdyLabels
combI=headSel2 #Starting Template orf, Genename columns
# headersRemc<-colnames(REMcRdy)
# Reorder columns to produce an interleaved set of Z_lm and Shift data for all the cpps.
for(i in 3:length(colnames(REMcRdy))){
combI=cbind.data.frame(combI, shiftOnly[i])
combI=cbind.data.frame(combI, REMcRdy[i])
}
Vec1=NA
Vec2=NA
Vec3=NA
Vec4=NA
Vec5=NA
Vec6=NA
Vec7=NA
Vec8=NA
if(length(REMcRdy)==6){
Vec1=abs(REMcRdy[,3])>=std
Vec2=abs(REMcRdy[,4])>=std
Vec3=abs(REMcRdy[,5])>=std
Vec4=abs(REMcRdy[,6])>=std
bolVec=Vec1 | Vec2 |Vec3 |Vec4
REMcRdyGT2=REMcRdy[bolVec,1:2]
REMcRdyGT2[ ,3:6]=REMcRdy[bolVec,3:6]
shiftOnlyGT2=shiftOnly[bolVec,1:2]
shiftOnlyGT2[ ,3:6]=shiftOnly[bolVec,3:6]
}
if(length(REMcRdy)==8){
Vec1=abs(REMcRdy[,3])>=std
Vec2=abs(REMcRdy[,4])>=std
Vec3=abs(REMcRdy[,5])>=std
Vec4=abs(REMcRdy[,6])>=std
Vec5=abs(REMcRdy[,7])>=std
Vec6=abs(REMcRdy[,8])>=std
bolVec=Vec1 | Vec2 |Vec3 | Vec4 |Vec5 |Vec6
REMcRdyGT2=REMcRdy[bolVec,1:2]
REMcRdyGT2[ ,3:8]=REMcRdy[bolVec,3:8]
shiftOnlyGT2=shiftOnly[bolVec,1:2]
shiftOnlyGT2[ ,3:8]=shiftOnly[bolVec,3:8]
}
if(length(REMcRdy)==10){
Vec1=abs(REMcRdy[,3])>=std
Vec2=abs(REMcRdy[,4])>=std
Vec3=abs(REMcRdy[,5])>=std
Vec4=abs(REMcRdy[,6])>=std
Vec5=abs(REMcRdy[,7])>=std
Vec6=abs(REMcRdy[,8])>=std
Vec7=abs(REMcRdy[,9])>=std
Vec8=abs(REMcRdy[,10])>=std
bolVec=Vec1 | Vec2 |Vec3 |Vec4|Vec5|Vec6|Vec7|Vec8
REMcRdyGT2=REMcRdy[bolVec,1:2]
REMcRdyGT2[ ,3:10]=REMcRdy[bolVec,3:10]
shiftOnlyGT2=shiftOnly[bolVec,1:2]
shiftOnlyGT2[ ,3:10]=shiftOnly[bolVec,3:10]
}
if(std!=0){
REMcRdy=REMcRdyGT2 # [,2:length(REMcRdyGT2)]
shiftOnly=shiftOnlyGT2 # [,2:length(shiftOnlyGT2)]
}
if(std==0){
REMcRdy=REMcRdy # [,2:length(REMcRdy)]
shiftOnly=shiftOnly # [,2:length(shiftOnly)]
}
# R places hidden "" around the header names. The following
# is intended to remove those quote so that the "" do not blow up the Java REMc.
# Use ,quote=F in the write.csv statement to fix R output file.
#write.csv(combI,file=file.path(outDir,"CombinedKLzscores.csv"),row.names=FALSE)
write.csv(REMcRdy,file=file.path(outDir,"REMcRdy_lm_only.csv"),row.names=FALSE, quote=F)
write.csv(shiftOnly,file=file.path(outDir,"Shift_only.csv"),row.names=FALSE, quote=F)
#LabelStd <- read.table(file="./parameters.csv",stringsAsFactors=FALSE,sep=",")
LabelStd<-read.csv(file=studyInfo,stringsAsFactors=FALSE)
print(std)
LabelStd[,4]=as.numeric(std)
write.csv(LabelStd,file=file.path(outDir,"parameters.csv"),row.names=FALSE)
write.csv(LabelStd,file=studyInfo,row.names=FALSE)
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