Merge branch 'master' into plink-converter-2024-03-26-tristanpwdennis-shadow

Author: jonbrenas

malariagen_data/anoph/frq_params.py

@@ -1,6 +1,6 @@
 """Parameter definitions for functions computing and plotting allele frequencies."""
 
-from typing import Literal
+from typing import Literal, List, Optional, Tuple, Union
 
 import xarray as xr
 from typing_extensions import Annotated, TypeAlias
@@ -70,3 +70,13 @@
     bool,
     "Include columns with allele counts and number of non-missing allele calls (nobs).",
 ]
+
+taxa: TypeAlias = Annotated[
+    Optional[Union[str, List[str], Tuple[str, ...]]],
+    "The taxon or taxa to restrict the dataset to.",
+]
+
+areas: TypeAlias = Annotated[
+    Optional[Union[str, List[str], Tuple[str, ...]]],
+    "The area or areas to restrict the dataset to.",
+]

malariagen_data/anoph/snp_frq.py

@@ -936,6 +936,8 @@ def plot_frequencies_time_series(
         legend_sizing: plotly_params.legend_sizing = "constant",
         show: plotly_params.show = True,
         renderer: plotly_params.renderer = None,
+        taxa: frq_params.taxa = None,
+        areas: frq_params.areas = None,
         **kwargs,
     ) -> plotly_params.figure:
         # Handle title.
@@ -947,6 +949,18 @@ def plot_frequencies_time_series(
         df_cohorts = ds[cohort_vars].to_dataframe()
         df_cohorts.columns = [c.split("cohort_")[1] for c in df_cohorts.columns]  # type: ignore
 
+        # If specified, restrict the dataframe by taxa.
+        if isinstance(taxa, str):
+            df_cohorts = df_cohorts[df_cohorts["taxon"] == taxa]
+        elif isinstance(taxa, (list, tuple)):
+            df_cohorts = df_cohorts[df_cohorts["taxon"].isin(taxa)]
+
+        # If specified, restrict the dataframe by areas.
+        if isinstance(areas, str):
+            df_cohorts = df_cohorts[df_cohorts["area"] == areas]
+        elif isinstance(areas, (list, tuple)):
+            df_cohorts = df_cohorts[df_cohorts["area"].isin(areas)]
+
         # Extract variant labels.
         variant_labels = ds["variant_label"].values
 

notebooks/plot_frequencies_space_time.ipynb

@@ -1,14 +1,22 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "47f669f3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import malariagen_data"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "f820bc66-2fb2-4ca2-9b54-824e50d61a0a",
    "metadata": {},
    "outputs": [],
    "source": [
-    "import malariagen_data\n",
-    "\n",
     "ag3 = malariagen_data.Ag3(\n",
     "    \"simplecache::gs://vo_agam_release_master_us_central1\",\n",
     "    simplecache=dict(cache_storage=\"../gcs_cache\"),\n",
@@ -23,8 +31,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import malariagen_data\n",
-    "\n",
     "af1 = malariagen_data.Af1(\n",
     "    \"simplecache::gs://vo_afun_release_master_us_central1\",\n",
     "    simplecache=dict(cache_storage=\"../gcs_cache\"),\n",
@@ -69,6 +75,26 @@
     "ag3.plot_frequencies_time_series(ds, height=500, width=1000)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "790c99e8",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ag3.plot_frequencies_time_series(ds, taxa=\"gambiae\", height=500, width=1000)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1bfc7298",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ag3.plot_frequencies_time_series(ds, taxa=(\"gambiae\", \"arabiensis\"), height=500, width=1000)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -252,6 +278,26 @@
     "ag3.plot_frequencies_time_series(ds, height=900, width=900)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e16ab3fe",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ag3.plot_frequencies_time_series(ds, areas=\"BF-09\", height=400, width=900)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "26af27a1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ag3.plot_frequencies_time_series(ds, areas=(\"BF-09\", \"TZ-25\"), height=400, width=900)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -336,19 +382,11 @@
    "source": [
     "af1.plot_frequencies_interactive_map(ds)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "a512b459",
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "mgen_data_py3.11",
    "language": "python",
    "name": "python3"
   },
@@ -362,7 +400,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.11.5"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

tests/anoph/test_snp_frq.py

@@ -1528,6 +1528,100 @@ def test_plot_frequencies_time_series(
     assert isinstance(fig, go.Figure)
 
 
+@parametrize_with_cases("fixture,api", cases=".")
+def test_plot_frequencies_time_series_with_taxa(
+    fixture,
+    api: AnophelesSnpFrequencyAnalysis,
+):
+    # Pick test parameters at random.
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = random.choice(all_sample_sets)
+    site_mask = random.choice(api.site_mask_ids + (None,))
+    transcript = random_transcript(api=api).name
+    area_by = random.choice(["country", "admin1_iso", "admin2_name"])
+    period_by = random.choice(["year", "quarter", "month"])
+
+    # Pick a random taxon and taxa from valid taxa.
+    sample_sets_taxa = (
+        api.sample_metadata(sample_sets=sample_sets)["taxon"].dropna().unique().tolist()
+    )
+    taxon = random.choice(sample_sets_taxa)
+    taxa = random.sample(sample_sets_taxa, random.randint(1, len(sample_sets_taxa)))
+
+    # Compute SNP frequencies.
+    ds = api.snp_allele_frequencies_advanced(
+        transcript=transcript,
+        area_by=area_by,
+        period_by=period_by,
+        sample_sets=sample_sets,
+        min_cohort_size=1,  # Don't exclude any samples.
+        site_mask=site_mask,
+    )
+
+    # Trim things down a bit for speed.
+    ds = ds.isel(variants=slice(0, 100))
+
+    # Plot with taxon.
+    fig = api.plot_frequencies_time_series(ds, show=False, taxa=taxon)
+
+    # Test taxon plot.
+    assert isinstance(fig, go.Figure)
+
+    # Plot with taxa.
+    fig = api.plot_frequencies_time_series(ds, show=False, taxa=taxa)
+
+    # Test taxa plot.
+    assert isinstance(fig, go.Figure)
+
+
+@parametrize_with_cases("fixture,api", cases=".")
+def test_plot_frequencies_time_series_with_areas(
+    fixture,
+    api: AnophelesSnpFrequencyAnalysis,
+):
+    # Pick test parameters at random.
+    all_sample_sets = api.sample_sets()["sample_set"].to_list()
+    sample_sets = random.choice(all_sample_sets)
+    site_mask = random.choice(api.site_mask_ids + (None,))
+    transcript = random_transcript(api=api).name
+    area_by = random.choice(["country", "admin1_iso", "admin2_name"])
+    period_by = random.choice(["year", "quarter", "month"])
+
+    # Compute SNP frequencies.
+    ds = api.snp_allele_frequencies_advanced(
+        transcript=transcript,
+        area_by=area_by,
+        period_by=period_by,
+        sample_sets=sample_sets,
+        min_cohort_size=1,  # Don't exclude any samples.
+        site_mask=site_mask,
+    )
+
+    # Trim things down a bit for speed.
+    ds = ds.isel(variants=slice(0, 100))
+
+    # Extract cohorts into a DataFrame.
+    cohort_vars = [v for v in ds if str(v).startswith("cohort_")]
+    df_cohorts = ds[cohort_vars].to_dataframe()
+
+    # Pick a random area and areas from valid areas.
+    cohorts_areas = df_cohorts["cohort_area"].dropna().unique().tolist()
+    area = random.choice(cohorts_areas)
+    areas = random.sample(cohorts_areas, random.randint(1, len(cohorts_areas)))
+
+    # Plot with area.
+    fig = api.plot_frequencies_time_series(ds, show=False, areas=area)
+
+    # Test areas plot.
+    assert isinstance(fig, go.Figure)
+
+    # Plot with areas.
+    fig = api.plot_frequencies_time_series(ds, show=False, areas=areas)
+
+    # Test area plot.
+    assert isinstance(fig, go.Figure)
+
+
 @parametrize_with_cases("fixture,api", cases=".")
 def test_plot_frequencies_interactive_map(
     fixture,