Fix: add sample_indices parameter to count_samples, plot_samples_interactive_map, plot_samples_bar, plot_sample_location_geo

Author: noir4201

malariagen_data/anoph/sample_metadata.py

@@ -815,6 +815,7 @@ def count_samples(
         sample_sets: Optional[base_params.sample_sets] = None,
         sample_query: Optional[base_params.sample_query] = None,
         sample_query_options: Optional[base_params.sample_query_options] = None,
+        sample_indices: Optional[base_params.sample_indices] = None,
         index: Union[str, Sequence[str]] = (
             "country",
             "admin1_iso",
@@ -829,6 +830,7 @@ def count_samples(
             sample_sets=sample_sets,
             sample_query=sample_query,
             sample_query_options=sample_query_options,
+            sample_indices=sample_indices,
         )
 
         # Create pivot table.
@@ -863,6 +865,7 @@ def plot_samples_interactive_map(
         sample_sets: Optional[base_params.sample_sets] = None,
         sample_query: Optional[base_params.sample_query] = None,
         sample_query_options: Optional[base_params.sample_query_options] = None,
+        sample_indices: Optional[base_params.sample_indices] = None,
         basemap: Optional[map_params.basemap] = map_params.basemap_default,
         center: map_params.center = map_params.center_default,
         zoom: map_params.zoom = map_params.zoom_default,
@@ -882,6 +885,7 @@ def plot_samples_interactive_map(
             sample_sets=sample_sets,
             sample_query=sample_query,
             sample_query_options=sample_query_options,
+            sample_indices=sample_indices,
         )
 
         # Pivot taxa by locations.
@@ -1191,6 +1195,7 @@ def plot_samples_bar(
         sample_sets: Optional[base_params.sample_sets] = None,
         sample_query: Optional[base_params.sample_query] = None,
         sample_query_options: Optional[base_params.sample_query_options] = None,
+        sample_indices: Optional[base_params.sample_indices] = None,
         template: plotly_params.template = "plotly_white",
         width: plotly_params.fig_width = 800,
         height: plotly_params.fig_height = 600,
@@ -1203,6 +1208,7 @@ def plot_samples_bar(
             sample_sets=sample_sets,
             sample_query=sample_query,
             sample_query_options=sample_query_options,
+            sample_indices=sample_indices,
         )
 
         # Special handling for plotting by year.
@@ -1673,6 +1679,7 @@ def plot_sample_location_geo(
         sample_sets: Optional[base_params.sample_sets],
         sample_query: Optional[base_params.sample_query] = None,
         sample_query_options: Optional[base_params.sample_query_options] = None,
+        sample_indices: Optional[base_params.sample_indices] = None,
         marker_size: plotly_params.marker_size = 10,
         color: plotly_params.color = "admin1_name",
         color_discrete_sequence: plotly_params.color_discrete_sequence = px.colors.qualitative.Prism,
@@ -1691,6 +1698,7 @@ def plot_sample_location_geo(
             sample_sets=sample_sets,
             sample_query=sample_query,
             sample_query_options=sample_query_options,
+            sample_indices=sample_indices,
         )
 
         # Set the location columns to use from the sample metadata.