Ensure that missing CNVs are shown in a different colour in plot_diplotype_clustering_advanced (#670)

* Trying something

* Updated the palette in plot_cnv_hmm

Author: jonbrenas

malariagen_data/anoph/cnv_data.py

@@ -825,7 +825,6 @@ def plot_cnv_hmm_heatmap_track(
         debug = self._log.debug
 
         import bokeh.models as bkmod
-        import bokeh.palettes as bkpal
         import bokeh.plotting as bkplt
 
         region_prepped: Region = parse_single_region(self, region)
@@ -892,7 +891,7 @@ def plot_cnv_hmm_heatmap_track(
         )
 
         debug("set up palette and color mapping")
-        palette = ("#cccccc",) + bkpal.PuOr5
+        palette = cnv_params.colorscale_default
         color_mapper = bkmod.LinearColorMapper(low=-1.5, high=4.5, palette=palette)
 
         debug("plot the HMM copy number data as an image")

malariagen_data/anoph/cnv_params.py

@@ -20,3 +20,6 @@
     `coverage_calls_analysis_ids` property for available values.
     """,
 ]
+
+# This is grey followed by PuOr5
+colorscale_default = ["#cccccc", "#5e3c99", "#b2abd2", "#f7f7f7", "#fdb863", "#e66101"]

malariagen_data/anoph/dipclust.py

@@ -425,16 +425,18 @@ def _dipclust_cnv_bar_trace(
             n if not pd.isna(n) else gene_ids[i] for i, n in enumerate(gene_names)
         ]
 
+        cn_mode_no_nan = np.nan_to_num(cn_mode, nan=-1)
+
         # Plot the copy number data.
         # N.B., here we have to use go.Heatmap directly rather than
         # px.imshow because the latter fails to incorporate zmin,
         # zmax and colorscale within the trace data, and so these
         # then get lost later when we try to combined into a single
         # figure.
         trace = go.Heatmap(
-            z=cn_mode,
+            z=cn_mode_no_nan,
             y=gene_labels,
-            zmin=0,
+            zmin=-1,
             zmax=4,
             colorscale=colorscale,
             showlegend=False,
@@ -564,7 +566,7 @@ def plot_diplotype_clustering_advanced(
         snp_filter_min_maf: float = 0.05,
         snp_query: Optional[base_params.snp_query] = AA_CHANGE_QUERY,
         cnv_region: Optional[base_params.regions] = None,
-        cnv_colorscale: plotly_params.color_continuous_scale = "PuOr_r",
+        cnv_colorscale: plotly_params.color_continuous_scale = cnv_params.colorscale_default,
         cnv_max_coverage_variance: cnv_params.max_coverage_variance = 0.2,
         site_mask: Optional[base_params.site_mask] = None,
         sample_sets: Optional[base_params.sample_sets] = None,