Fixed bug in heatmap R script (in case species name is not specified)

radseq_analysis/modules/analysis.py

@@ -21,12 +21,15 @@ def analysis(input_dir=None,
     parameters = Parameters(files_dir=input_dir,
                             output_file_path=output_file_path)
 
+    species = None
     if popmap_file_path:
         load_popmap(popmap_file_path, parameters)
         species = os.path.split(popmap_file_path)[1]
         species = os.path.splitext(species)[0]
-        species = '_'.join(s for s in species.split('_')[:-1])
-        parameters.species = species
+        if len(species.split('_')) > 1:
+            species = '_'.join(s for s in species.split('_')[:-1])
+
+    parameters.species = species
 
     if positions_file_path:
         load_positions_list(positions_file_path, parameters)

radseq_analysis/visualization/haplotypes.py

@@ -6,6 +6,7 @@ def haplotypes(input_file_path, output_file_path, species_name):
     scripts_d = ''.join(os.path.split(os.path.realpath(__file__))[:-1])
     cmd = ('Rscript ' + os.path.join(scripts_d, 'r_scripts', 'heatmap.R') +
            ' ' + input_file_path +
-           ' ' + output_file_path +
-           ' ' + species_name)
+           ' ' + output_file_path)
+    if species_name:
+        cmd += ' ' + species_name
     os.system(cmd)

radseq_analysis/visualization/r_scripts/heatmap.R

@@ -2,8 +2,12 @@
 args = commandArgs(trailingOnly=TRUE)
 
 # test if there is at least one argument: if not, return an error
-if (length(args) != 3){
-    stop("Usage: R frequencies.R input_file.tsv output_file.png species_name")
+if (length(args) > 3 | length(args) < 2){
+    stop("Usage: R heatmap.R input_file.tsv output_file.png [species_name]")
+} else if (length(args == 3)) {
+    species_name = args[3]
+} else if (length(args == 2)) {
+    species_name="none"
 }
 
 suppressMessages(require(readr))
@@ -11,7 +15,6 @@ suppressMessages(require(ggplot2))
 
 input_file_path = args[1]
 output_file_path = args[2]
-species_name = args[3]
 
 g_legend<-function(a.gplot){
     tmp <- ggplot_gtable(ggplot_build(a.gplot))