Subsampling Tutorial

docs/notebooks/subsampling.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Subsampling cells\n",
+    "In this tutorial we show how subsampling cells in scverse data objects can be done.\n",
+    "\n",
+    "\n",
+    "This is a placeholder to be filled."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd\n",
+    "import scanpy as sc\n",
+    "from imblearn.under_sampling import RandomUnderSampler"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "louvain\n",
+       "CD4 T cells          1144\n",
+       "CD14+ Monocytes       480\n",
+       "B cells               342\n",
+       "CD8 T cells           316\n",
+       "NK cells              154\n",
+       "FCGR3A+ Monocytes     150\n",
+       "Dendritic cells        37\n",
+       "Megakaryocytes         15\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "adata = sc.datasets.pbmc3k_processed()\n",
+    "adata.obs.louvain.value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/eljasroellin/Documents/scverse-tutorials/tutorials_venv_mar/lib/python3.11/site-packages/anndata/_core/aligned_df.py:67: ImplicitModificationWarning: Transforming to str index.\n",
+      "  warnings.warn(\"Transforming to str index.\", ImplicitModificationWarning)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "louvain\n",
+       "CD4 T cells          15\n",
+       "CD14+ Monocytes      15\n",
+       "B cells              15\n",
+       "CD8 T cells          15\n",
+       "NK cells             15\n",
+       "FCGR3A+ Monocytes    15\n",
+       "Dendritic cells      15\n",
+       "Megakaryocytes       15\n",
+       "Name: count, dtype: int64"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rus = RandomUnderSampler(random_state=0)\n",
+    "X_resampled, y_resampled = rus.fit_resample(adata.X, adata.obs.louvain)\n",
+    "adata_resampled = sc.AnnData(X_resampled, obs=pd.DataFrame(y_resampled))  ##adata[y_resampled]\n",
+    "adata_resampled.obs.louvain.value_counts()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "tutorials_venv_mar",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

tutorial-registry/tutorials/large-datasets/meta.yaml

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+name: Subsampling cells
+description: |
+  In this tutorial, we demonstrate subsampling with scverse data objects.
+link: # TODO https://scverse-tutorials.readthedocs.io/en/latest/notebooks/scverse_data_backed.html#working-with-scverse-objects-in-backed-mode
+primary_category: Large Datasets # Data structures
+image: icon.png
+tags:
+  - large datasets
+packages:
+  - anndata
+  - mudata
+  - scanpy
+authors:
+  - eroell