debug HBV_RNAs_count.R and push Docker xgrand/r-bolero:1.0

src/.docker_modules/r-bolero/1.0/HBV_RNAs_count.R

@@ -68,6 +68,7 @@ clean_SP <- identified_SP[!duplicated(identified_SP$id),] %>%
   select(id, mapQ, transcript_strand, JAQ, barcode, promoter, junction, SP_name)
 
 countSP <- clean_SP %>% count(SP_name)
+countSP$SP_name <- factor(countSP$SP_name)
 countSP <- dplyr::inner_join(palette_complete, 
                       countSP, 
                       by = c("nom" = "SP_name"))
@@ -78,6 +79,7 @@ countSP$nom <- factor(countSP$nom, levels = all_species_name)
 countSP <- dplyr::mutate(countSP,
                   proportion = (as.numeric(n)/sum(as.numeric(n))*100))
 #print(countSP)
+if (length(countSP$nom) != 0) {
   ggplot(countSP, aes(x = "percent", 
                       y = proportion,
                       fill = nom)) +
@@ -107,6 +109,7 @@ ggsave(file = paste0(opt$barcode, "_SP_proportion.png"),
          height = 1080,
          units = "px",
          dpi = 300)
+}
 
 # TSS not spliced:
 classified_reads <- read.table(file = opt$classification, 
@@ -235,6 +238,7 @@ count_clear <- clean_SP[clean_SP$SP_name %in% SPvariants,] %>% count(SP_name)
 count_clear <- dplyr::mutate(count_clear,
                       proportion=(as.numeric(n)/sum(as.numeric(n))*100))
 #print(count_clear)
+count_clear$SP_name <- factor(count_clear$SP_name)
 count_clear <- dplyr::inner_join(palette_complete,
                           count_clear, 
                           by = c("nom" = "SP_name"))