From b6bd968702b21f2cd8ed72be686d77a8666e2877 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Thu, 14 Oct 2021 12:18:13 +0300
Subject: bugfixes for script;create pheno and geno objects

---
 scripts/ctl_analysis.R | 36 +++++++++++++++++++++++++-----------
 1 file changed, 25 insertions(+), 11 deletions(-)

(limited to 'scripts/ctl_analysis.R')

diff --git a/scripts/ctl_analysis.R b/scripts/ctl_analysis.R
index d9a937f..8c831ad 100644
--- a/scripts/ctl_analysis.R
+++ b/scripts/ctl_analysis.R
@@ -1,4 +1,5 @@
 library(ctl)
+library(stringi);
 library(rjson)
 
 options(stringsAsFactors = FALSE);
@@ -7,6 +8,8 @@ options(stringsAsFactors = FALSE);
 
 args = commandArgs(trailingOnly=TRUE)
 
+imgDir = Sys.getenv("GENERATED_IMAGE_DIR")
+
 if (length(args)==0) {
   stop("Argument for the data file", call.=FALSE)
 } else {
@@ -14,20 +17,32 @@ if (length(args)==0) {
   json_file_path = args[1]
 }
 
+json_file_path
 # add validation for the files
 input <- fromJSON(file = json_file_path)
 
+genoData <- input$geno
+phenoData <- input$pheno
+
+formData <- input$form
+# create the matixes
+genoData
+geno_matrix = t(matrix(unlist(genoData$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))
 
-genotypes <- read.csv(input$geno_file,row.names=1, header=FALSE, sep="\t")
-# The phenotypes.csv file containing individuals (rows) x traits (columns) measurements:
-traits <- read.csv(input$pheno_file,row.names=1, header=FALSE, sep="\t")
+# Use a data frame to store the objects
+pheno = data.frame(pheno_matrix, check.names=FALSE)
+geno = data.frame(geno_matrix, check.names=FALSE)
 
 
-ctls <- CTLscan(geno,traits,strategy=input$strategy,
-	nperm=input$nperms,parametric =input$parametric,
-	nthreads=6,verbose=TRUE)
 
 
+ctls <- CTLscan(geno,pheno,verbose=TRUE)
+
 # same function used in a different script:refactor
 genImageRandStr <- function(prefix){
 
@@ -38,16 +53,15 @@ genImageRandStr <- function(prefix){
 
 
 #output matrix significant CTL interactions with 4 columns: trait, marker, trait, lod
-sign <- CTLsignificant(ctls,significance = input$significance)
+sign <- CTLsignificant(ctls,significance = formData$significance)
  
 # Create the lineplot
 imageLoc = file.path(imgDir,genImageRandStr("CTLline"))
 
 png(imageLoc,width=1000,height=600,type='cairo-png')
 
-lineplot(res, significance=input$significance)
-
+ctl.lineplot(ctls, significance=formData$significance)
 
-json_data <- list(significance=signs,
-	images=lists("image_1"=imageLoc),
+json_data <- list(significance=sign,
+	images=list("image_1"=imageLoc),
 	network_figure_location="/location")
\ No newline at end of file
-- 
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