Commit 52b183ad authored by khalid's avatar khalid
Browse files

add radsex_map_region plot

parent 0d010178
......@@ -10,10 +10,18 @@ chemin= paste0(parameters$results_dir,"/",parameters$<step_name>__radsex_map_out
chromosome_file = parameters$<step_name>__radsex_map_chromosome_file
fichiers = paste0(chemin, "/map_results.tsv")
output_file = paste(parameters$results_dir,parameters$<step_name>__radsex_map_output_dir,"Mapping_genome_radsex_map_mqc.png",sep = "/")
signi_out_file = paste(parameters$results_dir,parameters$<step_name>__radsex_map_output_dir,"signi_map_results_mqc.tsv",sep = "/")
# Default marker depths plot
if ( chromosome_file == ""){
radsex_map_circos(fichiers, output_file = output_file)
} else{
radsex_map_circos(fichiers, output_file = output_file, chromosomes_file= chromosome_file)
if (file.exists(signi_out_file) )
{
regions = read.table(signi_out_file, header= TRUE, sep="\t")
chromosomes = read.table(chromosome_file, header= FALSE, sep="\t")
reg = chromosomes[which(chomosomes[,1]==regions[1,2]),2]
radsex_map_region(fichiers, region = reg, chromosomes_file = chromosome_file, output_file = "mapping_to_first_contig_mqc.png")
}
}
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