diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/ctl_analysis.R | 14 |
1 files changed, 5 insertions, 9 deletions
diff --git a/scripts/ctl_analysis.R b/scripts/ctl_analysis.R index e43cd6c..00128be 100644 --- a/scripts/ctl_analysis.R +++ b/scripts/ctl_analysis.R @@ -66,7 +66,7 @@ genRandomFileName <- function(prefix,file_ext=".png"){ # #output matrix significant CTL interactions with 4 columns: trait, marker, trait, lod -ctl_significant <- CTLsignificant(ctls,significance = 0.05) +ctl_significant <- CTLsignificant(ctls,significance = input$significance) colnames(ctl_significant) = c("trait","marker","trait_2","LOD","dcor") @@ -78,7 +78,7 @@ imageLoc = file.path(input$imgDir,genRandomFileName("CTLline")) png(imageLoc,width=1000,height=600,type='cairo-png') -ctl.lineplot(ctls,significance = 0.05, gap = 50, +ctl.lineplot(ctls,significance = input$significance, gap = 50, col = "orange", bg.col = "lightgray", cex = 1, verbose = FALSE) dev.off() @@ -91,7 +91,7 @@ for (trait in phenoData$trait_db_list) { image_loc = file.path(input$imgDir,genRandomFileName(paste("CTL",n,sep=""))) png(image_loc,width=1000, height=600, type='cairo-png') - plot.CTLobject(ctls,n-1,significance= 0.05, main=paste("Phenotype",trait,sep="")) + plot.CTLobject(ctls,n-1,significance= input$significance, main=paste("Phenotype",trait,sep="")) ctl_plots = append(ctl_plots,image_loc) @@ -99,19 +99,15 @@ for (trait in phenoData$trait_db_list) n = n + 1 } -# rename coz of duplicate key names -# refactor this network_file_name = paste("ctlnet",stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"),sep="_") netfile = file.path(input$imgDir,paste(network_file_name,".sif",sep="")) nodefile = file.path(input$imgDir,paste(network_file_name,".nodes",sep="")) -# temp fix override ctlnetwork function to target gn2 use case - -# xtodo refactor function +# fn overrides ctlnetwork function to target gn2 use case CTLnetworkGn<- function(CTLobject, mapinfo, significance = 0.05, LODdrop = 2, what = c("names","ids"), short = FALSE, add.qtls = FALSE,verbose = TRUE){ if(missing(CTLobject) || is.null(CTLobject)) stop("argument 'CTLobject' is missing, with no default") @@ -211,7 +207,7 @@ CTLnetwork.addmarker <- function(markers, mapinfo, name, realname){ # generating network -ctl_network = CTLnetworkGn(ctls, significance = 0.05, LODdrop = 2,short = FALSE, add.qtls = FALSE, verbose = TRUE) +ctl_network = CTLnetworkGn(ctls, significance = input$significance, LODdrop = 2,short = FALSE, add.qtls = FALSE, verbose = TRUE) |