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Fix: add sample_indices parameter to count_samples, plot_samples_interactive_map, plot_samples_bar, plot_sample_location_geo #1127

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Merged
jonbrenas merged 3 commits into from
Mar 20, 2026
Merged

Fix: add sample_indices parameter to count_samples, plot_samples_interactive_map, plot_samples_bar, plot_sample_location_geo #1127

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86b2a0d
Fix: add sample_indices parameter to count_samples, plot_samples_inte…
noir4201 Mar 15, 2026
6efde4d
Merge branch 'master' into fix/sample-indices-missing-methods
jonbrenas Mar 20, 2026
509468c
Merge branch 'master' into fix/sample-indices-missing-methods
jonbrenas Mar 20, 2026
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8 changes: 8 additions & 0 deletions malariagen_data/anoph/sample_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -880,6 +880,7 @@ 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",
Expand All @@ -894,6 +895,7 @@ def count_samples(
sample_sets=sample_sets,
sample_query=sample_query,
sample_query_options=sample_query_options,
sample_indices=sample_indices,
)

# Create pivot table.
Expand Down Expand Up @@ -928,6 +930,7 @@ 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,
Expand All @@ -947,6 +950,7 @@ 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.
Expand Down Expand Up @@ -1256,6 +1260,7 @@ 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,
Expand All @@ -1268,6 +1273,7 @@ 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.
Expand Down Expand Up @@ -1768,6 +1774,7 @@ 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,
Expand All @@ -1786,6 +1793,7 @@ 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.
Expand Down
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