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Use the pivot table directly for taxa #1269

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Merged
jonbrenas merged 5 commits into from
Apr 3, 2026
Merged

Use the pivot table directly for taxa #1269

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1613f83
Use the pivot table directly for taxa
Apr 1, 2026
c68701b
Trying to sort out types
Apr 1, 2026
67d5667
Removed the other columns
Apr 1, 2026
95d0c3a
Moved the taxa thing
Apr 2, 2026
e7edb0f
Merge branch 'master' into GH1268-plot_samples_interactive_maps_bug_o…
jonbrenas Apr 3, 2026
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9 changes: 5 additions & 4 deletions malariagen_data/anoph/sample_metadata.py
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Original file line number Diff line number Diff line change
Expand Up @@ -971,6 +971,8 @@ def plot_samples_interactive_map(
fill_value=0,
)

taxa = df_pivot.columns.dropna().sort_values().unique()

# Append aggregations to pivot.
df_location_aggs = df_samples.groupby(location_composite_key).agg(
{
Expand Down Expand Up @@ -1015,7 +1017,6 @@ def plot_samples_interactive_map(
samples_map.layout.width = width

# Add markers.
count_factors = df_samples[count_by].dropna().sort_values().unique()
for _, row in df_pivot.reset_index().iterrows():
title = (
f"Location: {row.location} ({row.latitude:.3f}, {row.longitude:.3f})"
Expand All @@ -1028,13 +1029,13 @@ def plot_samples_interactive_map(
title += f"\nContributors: {row.contributor}"
title += "\nNo. specimens: "
all_n = 0
for factor in count_factors:
for taxon in taxa:
# Get the number of samples in this taxon
n = row[factor]
n = int(row[taxon])
# Count the number of samples in all taxa
all_n += n
if n > 0:
title += f"{n} {factor}; "
title += f"{n} {taxon}; "
# Only show a marker when there are enough samples
if all_n >= min_samples:
marker = ipyleaflet.Marker(
Expand Down
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