From 541af4ab39c911102fb89beedaa430e282bdb529 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Wed, 13 Oct 2021 14:50:03 +0300
Subject: export json data

---
 scripts/ctl_analysis.R | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

(limited to 'scripts')

diff --git a/scripts/ctl_analysis.R b/scripts/ctl_analysis.R
index 6c3b22f..24a86a8 100644
--- a/scripts/ctl_analysis.R
+++ b/scripts/ctl_analysis.R
@@ -2,10 +2,22 @@ library(ctl)
 
 # The genotypes.csv file containing the genotype matrix is stored individuals (rows) x genetic marker (columns):
 
+args = commandArgs(trailingOnly=TRUE)
 
-genotypes <- read.csv("genotypes.csv",row.names=1, header=FALSE, sep="\t")
+if (length(args)==0) {
+  stop("Argument for the geno and pheno file location is required", call.=FALSE)
+} else {
+  # default output file
+  geno_file  = args[1]
+  pheno_file = args[2]
+}
+
+
+
+
+genotypes <- read.csv(geno_file,row.names=1, header=FALSE, sep="\t")
 # The phenotypes.csv file containing individuals (rows) x traits (columns) measurements:
-traits <- read.csv("phenotypes.csv",row.names=1, header=FALSE, sep="\t")
+traits <- read.csv(pheno_file,row.names=1, header=FALSE, sep="\t")
 
 
 ctls <- CTLscan(geno,traits,strategy=input$strategy,
@@ -17,3 +29,9 @@ ctls <- CTLscan(geno,traits,strategy=input$strategy,
 #output matrix significant CTL interactions with 4 columns: trait, marker, trait, lod
 sign <- CTLsignificant(ctls,significance = input$significance)
 
+# add plots 
+
+
+json_data <- list(significance=signs,
+	images=lists("image_1":"image_location"),
+	network_figure_location="/location")
\ No newline at end of file
-- 
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