Add PAR option to 'diagram' and 'heatmap' commands (closes #872)

cnvlib/cnary.py

@@ -307,11 +307,11 @@ def shift_xx(self, is_haploid_x_reference=False, is_xx=None, diploid_parx_genome
             is_xx = self.guess_xx(is_haploid_x_reference=is_haploid_x_reference, diploid_parx_genome=diploid_parx_genome)
         if is_xx and is_haploid_x_reference:
             # Female: divide X coverages by 2 (in log2: subtract 1)
-            outprobes[outprobes.chromosome == self._chr_x_label, "log2"] -= 1.0
+            outprobes[outprobes.chromosome == self.chr_x_label, "log2"] -= 1.0
             # Male: no change
         elif not is_xx and not is_haploid_x_reference:
             # Male: multiply X coverages by 2 (in log2: add 1)
-            outprobes[outprobes.chromosome == self._chr_x_label, "log2"] += 1.0
+            outprobes[outprobes.chromosome == self.chr_x_label, "log2"] += 1.0
             # Female: no change
         return outprobes
 

cnvlib/commands.py

@@ -1449,6 +1449,7 @@ def _cmd_diagram(args):
     action="store_false",
     help="""Disable gene_name labels on plot (useful when a lot of CNV were called).""",
 )
+add_diploid_parx_genome(P_diagram)
 P_diagram.set_defaults(func=_cmd_diagram)
 
 
@@ -1747,6 +1748,7 @@ def _cmd_heatmap(args):
 P_heatmap_aes.add_argument(
     "-t", "--title", help="Plot title. [Default: Range if provided, otherwise none]"
 )
+add_diploid_parx_genome(P_heatmap)
 P_heatmap.set_defaults(func=_cmd_heatmap)