colour options for identity and similarity plots

KatyBrown · May 21, 2024 · 9a16ba6 · 9a16ba6
1 parent d0dc645
commit 9a16ba6
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Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/CIAlign/argP.py b/CIAlign/argP.py
@@ -535,11 +535,21 @@ def getParser():
                  help="""Matplotlib palette name for identity mini alignments. \
                  Default: %(default)s""")
 
+    optional.add("--plot_identity_gap_col", dest='plot_identity_gap_col',
+                 type=str, default='white',
+                 help="""Colour for gaps in identity mini alignments. \
+                 Default: %(default)s""")
+
     optional.add("--plot_similarity_palette", dest='plot_similarity_palette',
                  type=str, default='bone',
                  help="""Matplotlib palette name for similarity mini \
                  alignments. Default: %(default)s""")
 
+    optional.add("--plot_similarity_gap_col", dest='plot_similarity_gap_col',
+                 type=str, default='white',
+                 help="""Colour for gaps in similarity mini alignments. \
+                 Default: %(default)s""")
+
     optional.add("--plot_dpi", dest="plot_dpi",
                  type=int, default=300, metavar="(int)",
                  help="DPI for mini alignments. Default: %(default)s")

diff --git a/CIAlign/runCIAlign.py b/CIAlign/runCIAlign.py
@@ -902,7 +902,8 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
             height=args.plot_height,
             force_numbers=fn,
             palette=args.palette,
-            plot_identity_palette=args.plot_identity_palette)
+            plot_identity_palette=args.plot_identity_palette,
+            plot_identity_gap_col=args.plot_identity_gap_col)
     if args.plot_consensus_similarity:
         log.info("Plotting similarity to consensus")
         if not args.silent:
@@ -919,6 +920,7 @@ def runMiniAlignments(args, log, orig_arr, orig_nams, arr, nams,
             force_numbers=fn,
             palette=args.palette,
             plot_similarity_palette=args.plot_similarity_palette,
+            plot_similarity_gap_col=args.plot_similarity_gap_col,
             sub_matrix_name=args.plot_sub_matrix_name)