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Bryan Roessler
2024-08-13 15:27:53 -04:00
parent 724b292dab
commit f190967383
7 changed files with 367 additions and 298 deletions
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79
workflow/apps/r/addShiftVals.R
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@@ -7,7 +7,7 @@ library(plyr)
library(dplyr)
library(sos)
args=commandArgs(TRUE)
args <- commandArgs(TRUE)
if (length(args) >= 1) {
finalTable <- args[1]
@@ -30,62 +30,61 @@ if (length(args) >= 3) {
if (length(args) >= 4) {
output <- args[4]
} else {
output<- "REMcHeatmaps/REMcWithShift.csv" # for legacy workflow
output <- "REMcHeatmaps/REMcWithShift.csv" # for legacy workflow
}
# Read in the REMc finalTable data
X = data.frame(read.csv(file=finalTable,header=TRUE,stringsAsFactors = FALSE))
X <- data.frame(read.csv(file = finalTable, header = TRUE, stringsAsFactors = FALSE))
# Read in the shift data From ../JoinInteractions
Y = data.frame(read.csv(file=shiftFile,header=TRUE,stringsAsFactors = FALSE))
Labels <- read.delim(studyInfo,skip=0,as.is=T,row.names=1,strip.white=TRUE)
Y <- data.frame(read.csv(file = shiftFile, header = TRUE, stringsAsFactors = FALSE))
Labels <- read.delim(studyInfo, skip = 0, as.is = TRUE, row.names = 1, strip.white = TRUE)
# Determine the number of cols - needed to create the correct number of new cols
Xcolnum <- length(X[1,])
ADDnum <- Xcolnum + length(Y[1,]) - 2
Xcolnum <- length(X[1, ])
ADDnum <- Xcolnum + length(Y[1, ]) - 2
# Create new columns filled with NAs to be filled with data
Xtemp= X
Xtemp[,(Xcolnum+1):ADDnum] <- NA
Xtemp <- X
Xtemp[, (Xcolnum + 1):ADDnum] <- NA
# 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
shiftTbl <-as.data.frame(matrix(nrow=1,ncol=length(Y)-2)) #the df shiftTbl must be initialized before for loop
shiftTbl < - as.data.frame(matrix(nrow = 1, ncol = length(Y) - 2)) #the df shiftTbl must be initialized before for loop
for(i in 1:length(X[,1])){
Shiftrownum = match(X[i,2],Y[,1])
shiftTbl[i,]= Y[Shiftrownum,3:length(Y[1,])]
Xtemp[i,(Xcolnum+1):ADDnum] <- Y[Shiftrownum,3:length(Y[1,])]
for (i in 1:length(X[, 1])) {
Shiftrownum <- match(X[i, 2], Y[, 1])
shiftTbl[i, ] <- Y[Shiftrownum, 3:length(Y[1, ])]
Xtemp[i, (Xcolnum + 1):ADDnum] <- Y[Shiftrownum, 3:length(Y[1, ])]
}
headerX= colnames(Xtemp)
headerY= colnames(Y)
shfHdr= headerY[3:length(headerY)]
combTbl<- X[,1:3]
lmTbl= select(Xtemp, contains('Z_lm')) #X[,(4:Xcolnum-2)]
shiftTbl<- select(Xtemp, contains('V'))
clustTbl<- select(Xtemp, contains('cluster.'))
headerX <- colnames(Xtemp)
headerY <- colnames(Y)
shfHdr <- headerY[3:length(headerY)]
combTbl <- X[, 1:3]
lmTbl <- select(Xtemp, contains("Z_lm")) #X[,(4:Xcolnum-2)]
shiftTbl <- select(Xtemp, contains("V"))
clustTbl <- select(Xtemp, contains("cluster."))
# Give the new column names the same names as in the shift file
Xcols = colnames(X)
Ycols = colnames(Y)[3:length(Y[1,])]
newCols = c(Xcols[1:Xcolnum],Ycols)
Xcols <- colnames(X)
Ycols <- colnames(Y)[3:length(Y[1, ])]
newCols <- c(Xcols[1:Xcolnum], Ycols)
# Reorder columns for generating heatmaps
combI= combTbl #Starting Template orf, Genename columns
headersRemc<-newCols #colnames(X)
newHeaders= newCols[1:3]
lmHdr= colnames(lmTbl) #newCols[4:(length(Xcols)-2)]
clstHdr= colnames(clustTbl) #select(newCols, contains('cluster.')) #newCols[3+length(lmHdr):2]
combI <- combTbl #Starting Template orf, Genename columns
headersRemc <- newCols #colnames(X)
newHeaders <- newCols[1:3]
lmHdr <- colnames(lmTbl) #newCols[4:(length(Xcols)-2)]
clstHdr <- colnames(clustTbl) #select(newCols, contains('cluster.')) #newCols[3+length(lmHdr):2]
intLvHdr= vector()
intLvHdr <- vector()
#Reorder columns to produce an interleaved set of Z_lm and Shift data for all the cpps.
for(i in 1:(length(shiftTbl[1,]))){
combI=cbind.data.frame(combI, shiftTbl[i])
combI=cbind.data.frame(combI, lmTbl[i])
intLvHdrx= c(shfHdr[i],lmHdr[i] )
intLvHdr= c(intLvHdr,intLvHdrx)
for (i in 1:(length(shiftTbl[1, ]))) {
combI <- cbind.data.frame(combI, shiftTbl[i])
combI <- cbind.data.frame(combI, lmTbl[i])
intLvHdrx <- c(shfHdr[i], lmHdr[i])
intLvHdr <- c(intLvHdr, intLvHdrx)
}
combIHdr= c(colnames(combTbl),intLvHdr,clstHdr)
combI=cbind.data.frame(combI, clustTbl)
colnames(combI)= combIHdr
write.csv(combI,file=output, row.names=FALSE)
combIHdr <- c(colnames(combTbl), intLvHdr, clstHdr)
combI <- cbind.data.frame(combI, clustTbl)
colnames(combI) <- combIHdr
write.csv(combI, file = output, row.names = FALSE)