diff options
Diffstat (limited to 'scripts/rqtl2_wrapper.R')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 21 |
1 files changed, 20 insertions, 1 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index a2fbf1e..52877ae 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -207,5 +207,24 @@ return (out) results <- perform_genome_scan(cross=dataset, genome_prob=Pr, method = "HMM") -results +results # this should probably return the method use here + +# plot for the LOD scores from performing the genome scan + +generate_lod_plot <- function(cross, scan_result, method, base_dir="."){ +# Plot LOD curves for a genome scan +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_file_path <- generate_lod_plot(dataset, results, "HK") +lod_file_path \ No newline at end of file |