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library(ctl)
library(stringi);
library(rjson)
options(stringsAsFactors = FALSE);
# The genotypes.csv file containing the genotype matrix is stored individuals (rows) x genetic marker (columns):
args = commandArgs(trailingOnly=TRUE)
imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
if (length(args)==0) {
stop("Argument for the data file", call.=FALSE)
} else {
# default output file
json_file_path = args[1]
}
json_file_path
# add validation for the files
input <- fromJSON(file = json_file_path)
cat("The input data is \n")
genoData <- input$genoData
phenoData <- input$phenoData
# create the matixes
# genotypes Matrix of genotypes. (individuals x markers)
# phenotypes Matrix of phenotypes. (individuals x phenotypes)
geno_matrix = t(matrix(unlist(genoData$genotypes),
nrow=length(genoData$markernames), ncol=length(genoData$individuals),
dimnames=list(genoData$markernames, genoData$individuals), byrow=TRUE))
pheno_matrix = t(matrix(as.numeric(unlist(phenoData$traits)), nrow=length(phenoData$trait_db_list), ncol=length(
phenoData$individuals), dimnames= list(phenoData$trait_db_list, phenoData$individuals), byrow=TRUE))
# # Use a data frame to store the objects
ctls <- CTLscan(geno_matrix,pheno_matrix,nperm=input$nperm,strategy=input$strategy,parametric=TRUE,nthreads=3,verbose=TRUE)
# # same function used in a different script:refactor
genImageRandStr <- function(prefix){
randStr <- paste(prefix,stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_")
return(paste(randStr,".png",sep=""))
}
genRandomFileName <- function(prefix,file_ext=".png"){
randStr = paste(prefix,stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_")
return(paste(randStr,file_ext,sep=""))
}
# #output matrix significant CTL interactions with 4 columns: trait, marker, trait, lod
ctl_significant <- CTLsignificant(ctls,significance = 0.05)
colnames(ctl_significant) = c("trait","marker","trait_2","LOD","dcor")
# # Create the lineplot
imageLoc = file.path(input$imgDir,genRandomFileName("CTLline"))
png(imageLoc,width=1000,height=600,type='cairo-png')
ctl.lineplot(ctls,significance = 0.05, gap = 50,
col = "orange", bg.col = "lightgray", cex = 1, verbose = FALSE)
dev.off()
n = 2
ctl_plots = c()
for (trait in phenoData$trait_db_list)
{
image_loc = file.path(input$imgDir,genRandomFileName(paste("CTL",n,sep="")))
png(image_loc,width=1000, height=600, type='cairo-png')
plot.CTLobject(ctls,n-1,significance= 0.05, main=paste("Phenotype",trait,sep=""))
ctl_plots = append(ctl_plots,image_loc)
dev.off()
n = n + 1
}
# rename coz of duplicate key names
# refactor this
network_file_name = paste("ctlnet",stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_")
netfile = file.path(input$imgDir,paste(network_file_name,".sif",sep=""))
nodefile = file.path(input$imgDir,paste(network_file_name,".nodes",sep=""))
# temp fix override ctlnetwork function to target gn2 use case
# xtodo refactor function
CTLnetworkGn<- function(CTLobject, mapinfo, significance = 0.05, LODdrop = 2, what = c("names","ids"), short = FALSE, add.qtls = FALSE,verbose = TRUE){
if(missing(CTLobject) || is.null(CTLobject)) stop("argument 'CTLobject' is missing, with no default")
if("CTLscan" %in% class(CTLobject)) CTLobject = list(CTLobject)
if(length(what) > 1) what = what[1]
results <- NULL
significant <- CTLsignificant(CTLobject, significance, what = "ids")
if(!is.null(significant)){
all_m <- NULL; all_p <- NULL;
cat("",file=netfile); cat("",file=nodefile);
if(verbose) cat("NETWORK.SIF\n")
edges <- NULL
for(x in 1:nrow(significant)){
data <- as.numeric(significant[x,])
CTLscan <- CTLobject[[data[1]]]
markern <- rownames(CTLscan$dcor)
traitsn <- colnames(CTLscan$dcor)
name <- ctl.name(CTLscan)
if(what=="ids"){
tid <- which(traitsn %in% ctl.name(CTLobject[[data[1]]]))
name <- paste("P",tid,sep="")
markern <- paste("M",1:nrow(CTLobject[[data[1]]]$dcor), sep="")
traitsn <- paste("P", 1:ncol(CTLobject[[data[1]]]$dcor), sep="")
}
if(add.qtls){ # Add QTL to the output SIF
bfc <- length(CTLscan$qtl)
above <- which(CTLscan$qtl > -log10(significance))
qtlnms <- names(above); qtlmid <- 1
for(m in above){
cat(name,"\tQTL\t",markern[m],"\tQTL\t",CTLscan$qtl[m],"\n",sep="",file=netfile,append=TRUE)
all_m <- CTLnetwork.addmarker(all_m, mapinfo, markern[data[2]], qtlnms[qtlmid])
qtlmid <- qtlmid+1
}
}
lod <- CTLscan$ctl[data[2],data[3]]
qlod1 <- CTLscan$qtl[data[2]]
qlod2 <- qlod1
edgetype <- NA
if(length(CTLobject) >= data[3]){ # Edge type based on QTL LOD scores
qlod2 <- CTLobject[[data[3]]]$qtl[data[2]]
if((qlod1-qlod2) > LODdrop){
edgetype <- 1
}else if((qlod1-qlod2) < -LODdrop){
edgetype <- -1
}else{ edgetype <- 0; }
} else {
cat("Warning: Phenotype", data[3], "from", data[1], "no CTL/QTL information\n")
qlod2 <- NA;
}
#Store the results
results <- rbind(results, c(data[1], data[2], data[3], lod, edgetype, qlod1, qlod2))
if(nodefile == "" && !verbose){ }else{
if(short){
edge <- paste(name,traitsn[data[3]])
edgeI <- paste(traitsn[data[3]],name)
if(!edge %in% edges && !edgeI %in% edges){
cat(name, "\t", markern[data[2]],"\t", traitsn[data[3]],"\n",file=netfile, append=TRUE,sep="")
edges <- c(edges,edge)
}
}else{
cat(name, "\t", "CTL_", data[1],"_",data[3], "\t", markern[data[2]],file=netfile, append=TRUE,sep="")
cat("\tCTL\t", lod, "\n", file=netfile, append=TRUE,sep="")
cat(markern[data[2]], "\t", "CTL_", data[1],"_",data[3], "\t",file=netfile, append=TRUE,sep="")
cat(traitsn[data[3]],"\tCTL\t", lod, "\n", file=netfile,append=TRUE,sep="")
}
}
all_m <- CTLnetwork.addmarker(all_m, mapinfo, markern[data[2]], rownames(CTLscan$dcor)[data[2]])
all_p <- unique(c(all_p, name, traitsn[data[3]]))
}
colnames(results) <- c("TRAIT1","MARKER","TRAIT2","LOD_C","CAUSAL","LOD_T1","LOD_T2")
if(verbose) cat("NODE.DESCRIPTION\n")
if(nodefile == "" && !verbose){ }else{
for(m in all_m){ cat(m,"\n", sep="", file=nodefile, append=TRUE); }
for(p in all_p){ cat(p,"\tPHENOTYPE\n", sep="", file=nodefile, append=TRUE); }
}
}
if(!is.null(results)){
class(results) <- c(class(results),"CTLnetwork")
}
invisible(results)
}
CTLnetwork.addmarker <- function(markers, mapinfo, name, realname){
if(!missing(mapinfo)){
id <- which(rownames(mapinfo) %in% realname)
fname <- paste(name,"\tMARKER\t",mapinfo[id,1],"\t",mapinfo[id,2],sep="")
markers <- unique(c(markers, fname))
}
return(markers)
}
# generating network
ctl_network = CTLnetworkGn(ctls, significance = 0.05, LODdrop = 2,short = FALSE, add.qtls = FALSE, verbose = TRUE)
json_data <- list(phenotypes = input$phenoData$trait_db_list,significance_data = ctl_significant,image_loc = imageLoc,ctl_plots=ctl_plots,network_file_name = network_file_name)
json_data <- toJSON(json_data)
write(json_data,file= json_file_path)
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