Merge pull request #703 from malariagen/600-adding-option-for-multiple-transcripts-to-diplotype_clustering

Allow multiple SNP transcripts via snp_transcript in `plot_diplotype_clustering_advanced()`

Author: leehart

malariagen_data/anoph/dipclust.py

@@ -23,14 +23,16 @@
     cnv_params,
 )
 from .snp_frq import AnophelesSnpFrequencyAnalysis
-from .cnv_data import AnophelesCnvData
+from .cnv_frq import AnophelesCnvFrequencyAnalysis
 
 AA_CHANGE_QUERY = (
     "effect in ['NON_SYNONYMOUS_CODING', 'START_LOST', 'STOP_LOST', 'STOP_GAINED']"
 )
 
 
-class AnophelesDipClustAnalysis(AnophelesSnpFrequencyAnalysis, AnophelesCnvData):
+class AnophelesDipClustAnalysis(
+    AnophelesCnvFrequencyAnalysis, AnophelesSnpFrequencyAnalysis
+):
     def __init__(
         self,
         **kwargs,
@@ -190,7 +192,7 @@ def plot_diplotype_clustering(
         else:
             return {
                 "figure": fig,
-                "dendro_sample_id_order": leaf_data["sample_id"].to_list(),
+                "dendro_sample_id_order": np.asarray(leaf_data["sample_id"].to_list()),
                 "n_snps": n_snps_used,
             }
 
@@ -319,7 +321,7 @@ def _dipclust_het_bar_trace(
         sample_sets: Optional[base_params.sample_sets],
         sample_query: Optional[base_params.sample_query],
         sample_query_options: Optional[base_params.sample_query_options],
-        site_mask: base_params.site_mask,
+        site_mask: Optional[base_params.site_mask],
         cohort_size: Optional[base_params.cohort_size],
         random_seed: base_params.random_seed,
         color_continuous_scale: Optional[plotly_params.color_continuous_scale],
@@ -547,11 +549,52 @@ def _dipclust_concat_subplots(
 
         return fig
 
+    def _insert_dipclust_snp_trace(
+        self,
+        *,
+        figures,
+        subplot_heights,
+        snp_row_height: plotly_params.height = 25,
+        transcript: base_params.transcript,
+        snp_query: Optional[base_params.snp_query] = AA_CHANGE_QUERY,
+        sample_sets: Optional[base_params.sample_sets],
+        sample_query: Optional[base_params.sample_query],
+        sample_query_options: Optional[base_params.sample_query_options],
+        site_mask: Optional[base_params.site_mask],
+        dendro_sample_id_order: np.ndarray,
+        snp_filter_min_maf: float,
+        snp_colorscale: Optional[plotly_params.color_continuous_scale],
+        chunks: base_params.chunks = base_params.native_chunks,
+        inline_array: base_params.inline_array = base_params.inline_array_default,
+    ):
+        snp_trace, n_snps_transcript = self._dipclust_snp_trace(
+            transcript=transcript,
+            sample_sets=sample_sets,
+            sample_query=sample_query,
+            sample_query_options=sample_query_options,
+            snp_query=snp_query,
+            site_mask=site_mask,
+            dendro_sample_id_order=dendro_sample_id_order,
+            snp_filter_min_maf=snp_filter_min_maf,
+            snp_colorscale=snp_colorscale,
+            chunks=chunks,
+            inline_array=inline_array,
+        )
+
+        if snp_trace:
+            figures.append(snp_trace)
+            subplot_heights.append(snp_row_height * n_snps_transcript)
+        else:
+            print(
+                f"No SNPs were found below {snp_filter_min_maf} allele frequency. Omitting SNP genotype plot."
+            )
+        return figures, subplot_heights
+
     @doc(
         summary="Perform diplotype clustering, annotated with heterozygosity, gene copy number and amino acid variants.",
         parameters=dict(
             heterozygosity="Plot heterozygosity track.",
-            snp_transcript="Plot amino acid variants for this transcript.",
+            snp_transcript="Plot amino acid variants for these transcripts.",
             cnv_region="Plot gene CNV calls for this region.",
             snp_filter_min_maf="Filter amino acid variants with alternate allele frequency below this threshold.",
         ),
@@ -561,7 +604,7 @@ def plot_diplotype_clustering_advanced(
         region: base_params.regions,
         heterozygosity: bool = True,
         heterozygosity_colorscale: plotly_params.color_continuous_scale = "Greys",
-        snp_transcript: Optional[base_params.transcript] = None,
+        snp_transcript: Optional[dipclust_params.snp_transcript] = None,
         snp_colorscale: plotly_params.color_continuous_scale = "Greys",
         snp_filter_min_maf: float = 0.05,
         snp_query: Optional[base_params.snp_query] = AA_CHANGE_QUERY,
@@ -682,9 +725,11 @@ def plot_diplotype_clustering_advanced(
                 figures.append(cnv_trace)
                 subplot_heights.append(cnv_row_height * n_cnv_genes)
 
-        if snp_transcript:
-            snp_trace, n_snps_transcript = self._dipclust_snp_trace(
+        if isinstance(snp_transcript, str):
+            figures, subplot_heights = self._insert_dipclust_snp_trace(
                 transcript=snp_transcript,
+                figures=figures,
+                subplot_heights=subplot_heights,
                 sample_sets=sample_sets,
                 sample_query=sample_query,
                 sample_query_options=sample_query_options,
@@ -696,13 +741,22 @@ def plot_diplotype_clustering_advanced(
                 chunks=chunks,
                 inline_array=inline_array,
             )
-
-            if snp_trace:
-                figures.append(snp_trace)
-                subplot_heights.append(snp_row_height * n_snps_transcript)
-            else:
-                print(
-                    f"No SNPs were found below {snp_filter_min_maf} allele frequency. Omitting SNP genotype plot."
+        elif isinstance(snp_transcript, list):
+            for st in snp_transcript:
+                figures, subplot_heights = self._insert_dipclust_snp_trace(
+                    transcript=st,
+                    figures=figures,
+                    subplot_heights=subplot_heights,
+                    sample_sets=sample_sets,
+                    sample_query=sample_query,
+                    sample_query_options=sample_query_options,
+                    snp_query=snp_query,
+                    site_mask=site_mask,
+                    dendro_sample_id_order=dendro_sample_id_order,
+                    snp_filter_min_maf=snp_filter_min_maf,
+                    snp_colorscale=snp_colorscale,
+                    chunks=chunks,
+                    inline_array=inline_array,
                 )
 
         # Calculate total height based on subplot heights, plus a fixed

malariagen_data/anoph/dipclust_params.py

@@ -1,9 +1,17 @@
 """Parameters for diplotype clustering functions."""
 
+from typing_extensions import Annotated, TypeAlias, Union, Sequence
+
 from .distance_params import distance_metric
 from .clustering_params import linkage_method
+from .base_params import transcript
 
 
 linkage_method_default: linkage_method = "complete"
 
 distance_metric_default: distance_metric = "cityblock"
+
+snp_transcript: TypeAlias = Annotated[
+    Union[transcript, Sequence[transcript]],
+    "A transcript or a list of transcripts",
+]

malariagen_data/anopheles.py

@@ -12,11 +12,6 @@
 import plotly.graph_objects as go  # type: ignore
 from numpydoc_decorator import doc  # type: ignore
 
-from malariagen_data.anoph.snp_frq import (
-    AnophelesSnpFrequencyAnalysis,
-)
-
-from .anoph.cnv_frq import AnophelesCnvFrequencyAnalysis
 
 from .anoph import (
     aim_params,
@@ -32,7 +27,6 @@
 from .anoph.karyotype import AnophelesKaryotypeAnalysis
 from .anoph.aim_data import AnophelesAimData
 from .anoph.base import AnophelesBase
-from .anoph.cnv_data import AnophelesCnvData
 from .anoph.genome_features import AnophelesGenomeFeaturesData
 from .anoph.genome_sequence import AnophelesGenomeSequenceData
 from .anoph.hap_data import AnophelesHapData, hap_params
@@ -88,8 +82,6 @@ class AnophelesDataResource(
     AnophelesH12Analysis,
     AnophelesG123Analysis,
     AnophelesFstAnalysis,
-    AnophelesCnvFrequencyAnalysis,
-    AnophelesSnpFrequencyAnalysis,
     AnophelesHapFrequencyAnalysis,
     AnophelesDistanceAnalysis,
     AnophelesPca,
@@ -99,7 +91,6 @@ class AnophelesDataResource(
     AnophelesAimData,
     AnophelesHapData,
     AnophelesSnpData,
-    AnophelesCnvData,
     AnophelesSampleMetadata,
     AnophelesGenomeFeaturesData,
     AnophelesGenomeSequenceData,