diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/ctl_analysis.R | 13 |
1 files changed, 2 insertions, 11 deletions
diff --git a/scripts/ctl_analysis.R b/scripts/ctl_analysis.R index 9d27ffe..e06ac25 100644 --- a/scripts/ctl_analysis.R +++ b/scripts/ctl_analysis.R @@ -5,8 +5,6 @@ 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") @@ -14,7 +12,7 @@ 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] } @@ -48,14 +46,8 @@ geno_matrix = t(matrix(unlist(genoData$genotypes), pheno_matrix = t(matrix(as.numeric(unlist(phenoData$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=parametric,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="_") @@ -78,13 +70,12 @@ ctl_significant <- CTLsignificant(ctls,significance = input$significance) colnames(ctl_significant) = c("trait","marker","trait_2","LOD","dcor") -# # Create the lineplot - imageLoc = file.path(input$imgDir,genRandomFileName("CTLline")) png(imageLoc,width=1000,height=600,type='cairo-png') +# Create the lineplot ctl.lineplot(ctls,significance = input$significance, gap = 50, col = "orange", bg.col = "lightgray", cex = 1, verbose = FALSE) |