diff options
| -rw-r--r-- | scripts/ctl_analysis.R | 35 |
1 files changed, 17 insertions, 18 deletions
diff --git a/scripts/ctl_analysis.R b/scripts/ctl_analysis.R index ff7aa94..dd47759 100644 --- a/scripts/ctl_analysis.R +++ b/scripts/ctl_analysis.R @@ -59,6 +59,13 @@ genImageRandStr <- function(prefix){ } +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) @@ -69,7 +76,7 @@ colnames(ctl_significant) = c("trait","marker","trait_2","LOD","dcor") # # Create the lineplot -imageLoc = file.path(input$imgDir,genImageRandStr("CTLline")) +imageLoc = file.path(input$imgDir,genRandomFileName("CTLline")) png(imageLoc,width=1000,height=600,type='cairo-png') @@ -84,7 +91,7 @@ ctl_plots = c() for (trait in phenoData$trait_db_list) { - image_loc = file.path(input$imgDir,genImageRandStr(paste("CTL",n,sep=""))) + image_loc = file.path(input$imgDir,genRandomFileName(paste("CTL",n,sep=""))) png(image_loc,width=1000, height=600, type='cairo-png') plot.CTLobject(ctls,n-1,significance= 0.05, main=paste("Phenotype",trait,sep="")) @@ -97,18 +104,18 @@ for (trait in phenoData$trait_db_list) # rename coz of duplicate key names -network_file_path = file.path(input$imgDir,paste("ctlnet","randomz",sep="")) - +# refactor this -file.create(network_file_path) +network_file_name = paste("ctlnet",stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_") +netfile = file.path(input$imgDir,paste(network_file_name,".sif",sep="")) +nodefile = file.path(input$imgDir,paste(network_file_name,".nodes",sep="")) +# temp fix override ctlnetwork function to target gn2 use case +# xtodo refactor function -# temp fix override ctlnetwork function to target certain output file - - -CTLnetworkGn<- function(CTLobject, mapinfo, significance = 0.05, LODdrop = 2, what = c("names","ids"), short = FALSE, add.qtls = FALSE, file = "",tmpDir = "",verbose = TRUE){ +CTLnetworkGn<- function(CTLobject, mapinfo, significance = 0.05, LODdrop = 2, what = c("names","ids"), short = FALSE, add.qtls = FALSE,verbose = TRUE){ if(missing(CTLobject) || is.null(CTLobject)) stop("argument 'CTLobject' is missing, with no default") if("CTLscan" %in% class(CTLobject)) CTLobject = list(CTLobject) if(length(what) > 1) what = what[1] @@ -117,16 +124,8 @@ CTLnetworkGn<- function(CTLobject, mapinfo, significance = 0.05, LODdrop = 2, wh significant <- CTLsignificant(CTLobject, significance, what = "ids") if(!is.null(significant)){ all_m <- NULL; all_p <- NULL; - nodefile=""; netfile = ""; - if(file != ""){ - netfile = file.path(tmpDir,paste("ctlnet",file,".sif",sep="")) - nodefile = file.path(tmpDir,paste("ctlnet",file,".nodes",sep="")) - - # netfile <- paste("ctlnet",file,".sif",sep="") - # nodefile <- paste("ctlnet",file,".nodes",sep="") - } cat("",file=netfile); cat("",file=nodefile); if(verbose) cat("NETWORK.SIF\n") edges <- NULL @@ -214,7 +213,7 @@ CTLnetwork.addmarker <- function(markers, mapinfo, name, realname){ # generating network -ctl_network = CTLnetworkGn(ctls, significance = 0.05, LODdrop = 2,short = FALSE, add.qtls = FALSE,tmpDir=input$imgDir,file = "random", verbose = TRUE) +ctl_network = CTLnetworkGn(ctls, significance = 0.05, LODdrop = 2,short = FALSE, add.qtls = FALSE, verbose = TRUE) |