Update AMR_MGE.R

scripts/AMR_MGE.R

@@ -76,7 +76,14 @@ VirSorter$ContigID <- sprintf("%010d", VirSorter$ContigID)
 
 ## Combine Phage prediction
 Phage_prediction <- merge(VirFinder, VirSorter, by="ContigID", all = TRUE)
-Phage_prediction$VirSorter_prediction <- fct_explicit_na(Phage_prediction$VirSorter_prediction, na_level = "-")
+#Phage_prediction$VirSorter_prediction <- fct_explicit_na(Phage_prediction$VirSorter_prediction, na_level = "-")
+if(all(is.na(Phage_prediction$VirSorter_prediction))){
+       # issue #39
+       Phage_prediction$VirSorter_prediction <- factor(rep("-", nrow(Phage_prediction)))
+} else {
+       Phage_prediction$VirSorter_prediction <- fct_explicit_na(Phage_prediction$VirSorter_prediction, na_level = "-")
+}
+
 
 # Combine AMR/MGE with Phage prediction
 AMR_MGE <- merge(AMR_Plasmid, Phage_prediction, by="ContigID", all = TRUE)