diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 44 |
1 files changed, 0 insertions, 44 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 59467c6..275370b 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -327,49 +327,6 @@ if (cross$crosstype == "4way"){ scan_file <- file.path(opt$directory, "scan_results.csv") write.csv(scan_results, scan_file) -# function plot for the LOD scores from performing the genome scan -generate_lod_plot <- function(cross, scan_result, method, base_dir = ".") { - #' @description Plot LOD curves for a genome scan - #' @param the cross object - #' @param scan1 results - #' @param the method used to compute the scan1 results HK,LMM or LOCO - #' @param base_dir the path to write the generated plot - #' @return a string with the file path for the plot - cat("Generting the lod plot for the LOD scores\n") - color <- c("slateblue", "violetred", "green3") - par(mar = c(4.1, 4.1, 1.6, 1.1)) - ymx <- maxlod(scan_result) - file_name = genRandomFileName(prefix = "RQTL_LOD_SCORE_", file_ext = ".png") - image_loc = file.path(base_dir , file_name) - png(image_loc, - width = 1000, - height = 600, - type = 'cairo-png') - plot( - scan_result, - cross$gmap, - lodcolumn = 1, - col = color[1], - main = colnames(cross$pheno)[1], - ylim = c(0, ymx * 1.02) - ) - legend( - "topleft", - lwd = 2, - col = color[1], - method, - bg = "gray90", - lty = c(1, 1, 2) - ) - dev.off() - return (image_loc) -} - - -lod_plot_path <- generate_lod_plot(cross, scan_results, "HK", base_dir=opt$directory) -cat("Generated the lod plot at ", lod_plot_path, "\n") - - # function: perform permutation tests for single-QTL method perform_permutation_test <- function(cross, genome_prob, @@ -540,7 +497,6 @@ output = list(lod_peaks = lod_peaks, gmap_file = gmap_file, pmap_file = pmap_file, meffects_plots = meffects_plots, - lod_plot_path =lod_plot_path, permutations = NO_OF_PERMUTATION, scan_method = SCAN_METHOD ) |