Update WESopt_plot_results.R

scripts/WESopt_plot_results.R

@@ -145,7 +145,7 @@ plot_variants <- function(full.t, out_dir, plot_prefix, fill_by) {
 ###############
 ### General ###
 ###############
-wdir <- "WESopt"
+wdir <- "Fiumara_BasePrimeEd2022_WES/WESopt"
 
 out_dir <- paste(wdir, "results", sep = "/")
 dir.create(out_dir, showWarnings = F)
@@ -162,7 +162,7 @@ samples <- c("S1_B1", "S2_B2", "S3_B3",
 full.t <- data.frame()
 for (ss in samples) {
   print(ss)
-  t <- read.table(gzfile(paste(wdir, "data", ss, paste0(ss, "-DP500_PASS_sGQ80_sDP10.ANNOT.vcf.gz"), sep = "/")), comment.char = "#", sep = "\t")
+  t <- read.table(gzfile(paste(wdir, "data", paste0(ss, "-DP500_PASS_sGQ80_sDP10.ANNOT.vcf.gz"), sep = "/")), comment.char = "#", sep = "\t")
   colnames(t) <- c("CHROM","POS","ID","REF","ALT","QUAL","FILTER", "ANNOT", "FORMAT", "SAMPLE")
   t$Sample <- ss
   t$Vars <- paste(t$CHROM, t$POS, t$REF, t$ALT, sep = "-")