92 sor
2.9 KiB
R
92 sor
2.9 KiB
R
#!/usr/bin/env Rscript
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# This script will add the shift data to the finalTable.csv file
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#
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# May want to reorder columns in excel before making heatmaps - otherwise all the shift data will be plotted next to each other.
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library(plyr)
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library(dplyr)
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library(sos)
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args=commandArgs(TRUE)
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if (length(args) > 1) {
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finalTable <- args[1]
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} else {
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finalTable <- "REMcRdy_lm_only.csv-finalTable.csv" # for legacy workflow
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}
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if (length(args) > 2) {
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shiftFile <- args[2]
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} else {
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shiftFile <- "Shift_only.csv" # for legacy workflow
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}
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if (length(args) > 3) {
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studyInfo <- args[3]
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} else {
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studyInfo <- "../Code/StudyInfo.csv" # for legacy workflow
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}
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if (length(args) > 4) {
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output <- args[4]
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} else {
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output<- "REMcHeatmaps/REMcWithShift.csv" # for legacy workflow
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}
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# Read in the REMc finalTable data
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X = data.frame(read.csv(file=finalTable,header=TRUE,stringsAsFactors = FALSE))
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# Read in the shift data From ../JoinInteractions
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Y = data.frame(read.csv(file=shiftFile,header=TRUE,stringsAsFactors = FALSE))
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Labels <- read.delim(studyInfo,skip=0,as.is=T,row.names=1,strip.white=TRUE)
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# Determine the number of cols - needed to create the correct number of new cols
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Xcolnum <- length(X[1,])
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ADDnum <- Xcolnum + length(Y[1,]) - 2
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# Create new columns filled with NAs to be filled with data
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Xtemp= X
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Xtemp[,(Xcolnum+1):ADDnum] <- NA
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# Match the orf names in each row to a orf name in the shift data file and then add the shift data to the finalTable file
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shiftTbl <-as.data.frame(matrix(nrow=1,ncol=length(Y)-2)) #the df shiftTbl must be initialized before for loop
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for(i in 1:length(X[,1])){
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Shiftrownum = match(X[i,2],Y[,1])
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shiftTbl[i,]= Y[Shiftrownum,3:length(Y[1,])]
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Xtemp[i,(Xcolnum+1):ADDnum] <- Y[Shiftrownum,3:length(Y[1,])]
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}
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headerX= colnames(Xtemp)
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headerY= colnames(Y)
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shfHdr= headerY[3:length(headerY)]
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combTbl<- X[,1:3]
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lmTbl= select(Xtemp, contains('Z_lm')) #X[,(4:Xcolnum-2)]
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shiftTbl<- select(Xtemp, contains('V'))
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clustTbl<- select(Xtemp, contains('cluster.'))
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# Give the new column names the same names as in the shift file
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Xcols = colnames(X)
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Ycols = colnames(Y)[3:length(Y[1,])]
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newCols = c(Xcols[1:Xcolnum],Ycols)
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# Reorder columns for generating heatmaps
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combI= combTbl #Starting Template orf, Genename columns
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headersRemc<-newCols #colnames(X)
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newHeaders= newCols[1:3]
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lmHdr= colnames(lmTbl) #newCols[4:(length(Xcols)-2)]
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clstHdr= colnames(clustTbl) #select(newCols, contains('cluster.')) #newCols[3+length(lmHdr):2]
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intLvHdr= vector()
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#Reorder columns to produce an interleaved set of Z_lm and Shift data for all the cpps.
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for(i in 1:(length(shiftTbl[1,]))){
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combI=cbind.data.frame(combI, shiftTbl[i])
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combI=cbind.data.frame(combI, lmTbl[i])
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intLvHdrx= c(shfHdr[i],lmHdr[i] )
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intLvHdr= c(intLvHdr,intLvHdrx)
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}
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combIHdr= c(colnames(combTbl),intLvHdr,clstHdr)
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combI=cbind.data.frame(combI, clustTbl)
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colnames(combI)= combIHdr
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write.csv(combI,file=output, row.names=FALSE)
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