diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 18 |
1 files changed, 17 insertions, 1 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index a4fcbfb..f2d6a87 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -497,16 +497,32 @@ covar meffects <- c() +meffects_plots <- c() + # TODO add plots for meffects for (chr in chr_names(dataset)){ cat("Getting the qtl effect for chromosome", chr) cat("\n") if (dataset$crosstype == "4way"){ coeff_results <- get_qtl_effect(chr, aPr, pheno, LOCO="LOCO", covar = sex) + file_name = genRandomFileName(prefix = "RQTL_EFFECT_", file_ext = ".png") + image_loc = file.path(base_dir , file_name) + par(mar=c(4.1, 4.1, 0.6, 0.6)) + png(image_loc, + width = 1000, + height = 600, + type = 'cairo-png') + plot( + coeff_results, + cross$gmap[chr], + bgcolor="gray95", + legend="bottomleft" + ) + meffects <- append(meffects_plots, image_loc) } else { coeff_results <- get_qtl_effect(chr, Pr, pheno) } - + meffects <- append(meffects, coeff_results) } |