avoid error with empty contamination input

broadinstitute · Nov 12, 2023 · c1857a4 · c1857a4
1 parent b4743a4
commit c1857a4
Showing 1 changed file with 7 additions and 2 deletions.
diff --git a/bin/visualize_plate_map.R b/bin/visualize_plate_map.R
@@ -184,8 +184,13 @@ if(input_file_type == "contamination")
   {
     input_table$contamination_source_well <- input_table$potential_contaminating_sample_plate_position
   }
-  input_table$Row0 <- as.numeric(lapply(gsub("[[:digit:]]","",input_table$contamination_source_well), FUN=row_letters_to_row_number)) # retrieves letters, converts to digits
-  input_table$Column0 <- as.numeric(gsub("[^[:digit:]]", "", input_table$contamination_source_well)) # retrieves digits
+  input_table$Row0 <- NULL
+  input_table$Column0 <- NULL
+  if(nrow(input_table) > 0)
+  {
+    input_table$Row0 <- as.numeric(lapply(gsub("[[:digit:]]","",input_table$contamination_source_well), FUN=row_letters_to_row_number)) # retrieves letters, converts to digits
+    input_table$Column0 <- as.numeric(gsub("[^[:digit:]]", "", input_table$contamination_source_well)) # retrieves digits
+  }
 
   # determines amount to jitter--more jitter if more lines of potential cross-contamination
   MIN_JITTER <- 0