Plot counts per recombinant lineage/t-SNE cluster

Related to #92
blab · Apr 26, 2024 · 5d438e3 · 5d438e3
1 parent 43916cd
commit 5d438e3
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diff --git a/sars-cov-2-nextstrain-2022-2023/Snakefile b/sars-cov-2-nextstrain-2022-2023/Snakefile
@@ -908,6 +908,7 @@ rule sarscov2_test_create_notebook_docs:
         PCA_Supplement_PNG="manuscript/figures/sarscov2-test-pca-by-{clade_membership}-clade.png",
         MDS_Supplement="manuscript/figures/sarscov2-test-mds-by-{clade_membership}-clade.html",
         MDS_Supplement_PNG="manuscript/figures/sarscov2-test-mds-by-{clade_membership}-clade.png",
+        tsne_recombinant_counts="manuscript/figures/sarscov2-test-tsne-recombinant-counts-{clade_membership}.png",
     params:
         clade_membership=lambda wildcards: wildcards.clade_membership,
         pca_label=lambda wildcards: f"pca_label_for_{wildcards.clade_membership}",

diff --git a/sars-cov-2-nextstrain/2022-03-29-final-figures.py.ipynb b/sars-cov-2-nextstrain/2022-03-29-final-figures.py.ipynb
@@ -71,7 +71,9 @@
     "static_pca_chart = snakemake.output.PCA_Supplement_PNG\n",
     "\n",
     "interactive_mds_chart = snakemake.output.MDS_Supplement\n",
-    "static_mds_chart = snakemake.output.MDS_Supplement_PNG"
+    "static_mds_chart = snakemake.output.MDS_Supplement_PNG\n",
+    "\n",
+    "output_tsne_recombinant_counts_png = snakemake.output.tsne_recombinant_counts"
    ]
   },
   {
@@ -1132,6 +1134,163 @@
     "full_chart_by_cluster.save(static_chart_by_clusters, format=\"png\", scale_factor=2.0)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4ca62b00",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tsne_label_column = [column for column in embeddings_df.columns if column.startswith(\"t-sne_label\")][0]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8059ea3a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tsne_label_column"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a15fbda6",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b2f3af09",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "embeddings_df[tsne_label_column] != -1"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a548586a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "(embeddings_df[\"Nextclade_pango_collapsed\"].str.startswith(\"X\").fillna(False))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bfa689b3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "embeddings_df.loc[embeddings_df[\"is_internal_node\"] == False]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b249281c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tsne_recombinant_counts = embeddings_df.loc[\n",
+    "    (\n",
+    "        (embeddings_df[\"is_internal_node\"] == False) &\n",
+    "        (embeddings_df[\"Nextclade_pango_collapsed\"].str.startswith(\"X\").fillna(False)) &\n",
+    "        (embeddings_df[tsne_label_column] != -1)\n",
+    "    ),\n",
+    "    [\n",
+    "        \"Nextclade_pango_collapsed\",\n",
+    "        tsne_label_column,\n",
+    "    ]\n",
+    "].value_counts().reset_index(name=\"count\").query(\"count >= 10\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ae75274e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tsne_recombinant_counts.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d0670bb6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tsne_recombinant_counts_chart = alt.Chart(tsne_recombinant_counts).mark_circle().encode(\n",
+    "    x=alt.X(\"Nextclade_pango_collapsed:N\", title=\"Recombinant Pango lineage\"),\n",
+    "    y=alt.Y(f\"{tsne_label_column}:N\", title=\"Cluster from t-SNE\"),\n",
+    "    size=\"count:Q\",\n",
+    "    tooltip=[\"Nextclade_pango_collapsed:N\", f\"{tsne_label_column}:N\", \"count:Q\"],\n",
+    ").properties(\n",
+    "    width=600,\n",
+    "    height=600,\n",
+    ")\n",
+    "tsne_recombinant_counts_chart"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9f4dad63",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tsne_recombinant_counts_chart.save(output_tsne_recombinant_counts_png, format=\"png\", scale_factor=2.0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ee0c9198",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tsne_recombinant_counts[\"Nextclade_pango_collapsed\"].value_counts().shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "56c46ef2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "(tsne_recombinant_counts[\"Nextclade_pango_collapsed\"].value_counts() == 1).sum()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e0b7d48f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "tsne_recombinant_counts[tsne_label_column].value_counts().shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "942f5d1f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "(tsne_recombinant_counts[tsne_label_column].value_counts() == 1).sum()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "e303df26",