Rename plot_genes() labels param to gene_labelset everywhere

malariagen · Nov 28, 2024 · f1b1b35 · f1b1b35
1 parent ed16b06
commit f1b1b35
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Showing 10 changed files with 32 additions and 32 deletions.
diff --git a/malariagen_data/anoph/cnv_data.py b/malariagen_data/anoph/cnv_data.py
@@ -752,7 +752,7 @@ def plot_cnv_hmm_coverage(
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         debug = self._log.debug
 
@@ -785,7 +785,7 @@ def plot_cnv_hmm_coverage(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         debug("combine plots into a single figure")
@@ -965,7 +965,7 @@ def plot_cnv_hmm_heatmap(
         genes_height: gplt_params.genes_height = gplt_params.genes_height_default,
         show: gplt_params.show = True,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         debug = self._log.debug
 
@@ -996,7 +996,7 @@ def plot_cnv_hmm_heatmap(
             x_range=fig1.x_range,
             show=False,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         debug("combine plots into a single figure")

diff --git a/malariagen_data/anoph/fst.py b/malariagen_data/anoph/fst.py
@@ -294,7 +294,7 @@ def plot_fst_gwss(
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
         clip_min: fst_params.clip_min = 0.0,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         # gwss track
         fig1 = self.plot_fst_gwss_track(
@@ -330,7 +330,7 @@ def plot_fst_gwss(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         # combine plots into a single figure

diff --git a/malariagen_data/anoph/g123.py b/malariagen_data/anoph/g123.py
@@ -439,7 +439,7 @@ def plot_g123_gwss(
         inline_array: base_params.inline_array = base_params.inline_array_default,
         chunks: base_params.chunks = base_params.native_chunks,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         # gwss track
         fig1 = self.plot_g123_gwss_track(
@@ -475,7 +475,7 @@ def plot_g123_gwss(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         # combine plots into a single figure

diff --git a/malariagen_data/anoph/genome_features.py b/malariagen_data/anoph/genome_features.py
@@ -334,7 +334,7 @@ def plot_genes(
         title: Optional[gplt_params.title] = None,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         debug = self._log.debug
 
@@ -502,8 +502,8 @@ def plot_genes(
             fig.add_layout(gene_pointers_ls)
             fig.add_layout(gene_labels_ls)
 
-        if labels:
-            fig.add_layout(labels)
+        if gene_labelset:
+            fig.add_layout(gene_labelset)
 
         debug("tidy up the plot")
         fig.ygrid.visible = False

diff --git a/malariagen_data/anoph/gplt_params.py b/malariagen_data/anoph/gplt_params.py
@@ -126,7 +126,7 @@
     "A mapping of gene identifiers to custom labels, which will appear in the plot.",
 ]
 
-labels: TypeAlias = Annotated[
+gene_labelset: TypeAlias = Annotated[
     bokeh.models.LabelSet,
     "A LabelSet to use in the plot.",
 ]
diff --git a/malariagen_data/anoph/h12.py b/malariagen_data/anoph/h12.py
@@ -474,7 +474,7 @@ def plot_h12_gwss(
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         # Plot GWSS track.
         fig1 = self.plot_h12_gwss_track(
@@ -511,7 +511,7 @@ def plot_h12_gwss(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         # Combine plots into a single figure.
@@ -679,7 +679,7 @@ def plot_h12_gwss_multi_overlay(
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         # Plot GWSS track.
         fig1 = self.plot_h12_gwss_multi_overlay_track(
@@ -717,7 +717,7 @@ def plot_h12_gwss_multi_overlay(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         # Combine plots into a single figure.
@@ -764,7 +764,7 @@ def plot_h12_gwss_multi_panel(
         show: gplt_params.show = True,
         output_backend: gplt_params.output_backend = gplt_params.output_backend_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         cohort_queries = self._setup_cohort_queries(
             cohorts=cohorts,
@@ -818,7 +818,7 @@ def plot_h12_gwss_multi_panel(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         figs.append(fig2)

diff --git a/malariagen_data/anoph/h1x.py b/malariagen_data/anoph/h1x.py
@@ -306,7 +306,7 @@ def plot_h1x_gwss(
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         # Plot GWSS track.
         fig1 = self.plot_h1x_gwss_track(
@@ -344,7 +344,7 @@ def plot_h1x_gwss(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         # Combine plots into a single figure.

diff --git a/malariagen_data/anoph/snp_data.py b/malariagen_data/anoph/snp_data.py
@@ -1306,7 +1306,7 @@ def plot_snps(
         max_snps: int = 200_000,
         show: gplt_params.show = True,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         # Plot SNPs track.
         fig1 = self.plot_snps_track(
@@ -1333,7 +1333,7 @@ def plot_snps(
             x_range=fig1.x_range,
             show=False,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         # Layout tracks in a grid.

diff --git a/malariagen_data/anopheles.py b/malariagen_data/anopheles.py
@@ -430,7 +430,7 @@ def plot_heterozygosity(
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         debug = self._log.debug
 
@@ -492,7 +492,7 @@ def plot_heterozygosity(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
         figs.append(fig_genes)
 
@@ -729,7 +729,7 @@ def plot_roh(
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         debug = self._log.debug
 
@@ -803,7 +803,7 @@ def plot_roh(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
         figs.append(fig_genes)
 
@@ -2297,7 +2297,7 @@ def plot_xpehh_gwss(
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         # gwss track
         fig1 = self.plot_xpehh_gwss_track(
@@ -2343,7 +2343,7 @@ def plot_xpehh_gwss(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         # combine plots into a single figure
@@ -2402,7 +2402,7 @@ def plot_ihs_gwss(
         chunks: base_params.chunks = base_params.native_chunks,
         inline_array: base_params.inline_array = base_params.inline_array_default,
         gene_labels: Optional[gplt_params.gene_labels] = None,
-        labels: Optional[gplt_params.labels] = None,
+        gene_labelset: Optional[gplt_params.gene_labelset] = None,
     ) -> gplt_params.figure:
         # gwss track
         fig1 = self.plot_ihs_gwss_track(
@@ -2450,7 +2450,7 @@ def plot_ihs_gwss(
             show=False,
             output_backend=output_backend,
             gene_labels=gene_labels,
-            labels=labels,
+            gene_labelset=gene_labelset,
         )
 
         # combine plots into a single figure

diff --git a/notebooks/plot_genes.ipynb b/notebooks/plot_genes.ipynb
@@ -272,7 +272,7 @@
     "  ]\n",
     ")\n",
     "data_as_cds = bokeh.models.ColumnDataSource(data)\n",
-    "labels = bokeh.models.LabelSet(\n",
+    "gene_labelset = bokeh.models.LabelSet(\n",
     "    source=data_as_cds,\n",
     "    x='pos',\n",
     "    y='y',\n",
@@ -285,7 +285,7 @@
     "\n",
     "ag3.plot_genes(\n",
     "  region=\"2R\",\n",
-    "  labels=labels,\n",
+    "  gene_labelset=gene_labelset,\n",
     "  height=200,\n",
     ")"
    ]