docs/notebooks/breast_cancer.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Breast cancer data showcase"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/wojciechlason/miniconda3/envs/dge-hackhaton/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
      "  from .autonotebook import tqdm as notebook_tqdm\n",
      "OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.\n"
     ]
    }
   ],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "from multi_condition_comparisions.tl.de import StatsmodelsDE\n",
    "\n",
    "import decoupler as dc\n",
    "import scanpy as sc"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The breast cancer single nuclei dataset was downloaded from cellxgene."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import cellxgene_census\n",
    "\n",
    "cellxgene_census.download_source_h5ad(\"cd74e95e-6583-4875-a0ba-f2eae5a1e5a6.h5ad\", to_path=\"breast_cancer.h5ad\")\n",
    "\n",
    "adata = sc.read_h5ad(\"./cd74e95e-6583-4875-a0ba-f2eae5a1e5a6.h5ad\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "adata.layers[\"counts\"] = adata.raw.X\n",
    "adata.layers[\"normalised_counts\"] = adata.X"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<bound method AnnData.obs_keys of AnnData object with n_obs × n_vars = 117346 × 33234\n",
       "    obs: 'mapped_reference_assembly', 'mapped_reference_annotation', 'alignment_software', 'donor_id', 'self_reported_ethnicity_ontology_term_id', 'donor_living_at_sample_collection', 'donor_menopausal_status', 'organism_ontology_term_id', 'sample_uuid', 'sample_preservation_method', 'tissue_ontology_term_id', 'development_stage_ontology_term_id', 'sample_derivation_process', 'sample_source', 'donor_BMI_at_collection', 'suspension_derivation_process', 'suspension_dissociation_reagent', 'suspension_uuid', 'suspension_type', 'library_uuid', 'assay_ontology_term_id', 'library_starting_quantity', 'sequencing_platform', 'is_primary_data', 'cell_type_ontology_term_id', 'author_cell_type', 'disease_ontology_term_id', 'sex_ontology_term_id', 'procedure_group', 'tissue_location', 'nCount_RNA', 'nFeature_RNA', 'percent.mito', 'sample_id', 'age_group', 'bmi_group', 'breast_density', 'cell_type', 'assay', 'disease', 'organism', 'sex', 'tissue', 'self_reported_ethnicity', 'development_stage'\n",
       "    var: 'feature_is_filtered', 'vst.mean', 'vst.variance', 'vst.variance.expected', 'vst.variance.standardized', 'feature_name', 'feature_reference', 'feature_biotype'\n",
       "    uns: 'default_embedding', 'schema_version', 'title'\n",
       "    obsm: 'X_umap'\n",
       "    layers: 'counts', 'normalised_counts'>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata.obs_keys"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/wojciechlason/miniconda3/envs/dge-hackhaton/lib/python3.10/site-packages/decoupler/utils_anndata.py:181: FutureWarning: The default of observed=False is deprecated and will be changed to True in a future version of pandas. Pass observed=False to retain current behavior or observed=True to adopt the future default and silence this warning.\n",
      "  cols = obs.groupby([sample_col, groups_col]).apply(lambda x: x.apply(lambda y: len(y.unique()) == 1)).all(0)\n",
      "/Users/wojciechlason/miniconda3/envs/dge-hackhaton/lib/python3.10/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.\n",
      "  warnings.warn(\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 183 × 30735\n",
       "    obs: 'mapped_reference_assembly', 'mapped_reference_annotation', 'alignment_software', 'donor_id', 'self_reported_ethnicity_ontology_term_id', 'donor_living_at_sample_collection', 'donor_menopausal_status', 'organism_ontology_term_id', 'sample_preservation_method', 'tissue_ontology_term_id', 'development_stage_ontology_term_id', 'sample_derivation_process', 'sample_source', 'donor_BMI_at_collection', 'suspension_derivation_process', 'suspension_dissociation_reagent', 'suspension_type', 'assay_ontology_term_id', 'library_starting_quantity', 'sequencing_platform', 'is_primary_data', 'cell_type_ontology_term_id', 'disease_ontology_term_id', 'sex_ontology_term_id', 'procedure_group', 'age_group', 'bmi_group', 'breast_density', 'cell_type', 'assay', 'disease', 'organism', 'sex', 'tissue', 'self_reported_ethnicity', 'development_stage', 'psbulk_n_cells', 'psbulk_counts'\n",
       "    var: 'feature_is_filtered', 'vst.mean', 'vst.variance', 'vst.variance.expected', 'vst.variance.standardized', 'feature_name', 'feature_reference', 'feature_biotype'\n",
       "    layers: 'psbulk_props'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pbulk = dc.get_pseudobulk(\n",
    "    adata,\n",
    "    sample_col=\"donor_id\",\n",
    "    groups_col=\"cell_type\",\n",
    "    layer=\"normalised_counts\",\n",
    "    mode=\"sum\",\n",
    "    min_cells=10,\n",
    "    min_counts=1000,\n",
    ")\n",
    "\n",
    "pbulk"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "mod = StatsmodelsDE(pbulk, \"~ disease:cell_type\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 30735/30735 [01:42<00:00, 298.45it/s]\n"
     ]
    }
   ],
   "source": [
    "mod.fit()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Intercept</th>\n",
       "      <th>cell_type[T.adipocyte of breast]</th>\n",
       "      <th>cell_type[T.basal cell]</th>\n",
       "      <th>cell_type[T.endothelial cell of lymphatic vessel]</th>\n",
       "      <th>cell_type[T.endothelial cell of vascular tree]</th>\n",
       "      <th>cell_type[T.fibroblast]</th>\n",
       "      <th>cell_type[T.luminal epithelial cell of mammary gland]</th>\n",
       "      <th>cell_type[T.mast cell]</th>\n",
       "      <th>cell_type[T.myeloid cell]</th>\n",
       "      <th>cell_type[T.pericyte]</th>\n",
       "      <th>disease[T.normal]:cell_type[T.T cell]</th>\n",
       "      <th>disease[T.normal]:cell_type[T.adipocyte of breast]</th>\n",
       "      <th>disease[T.normal]:cell_type[T.basal cell]</th>\n",
       "      <th>disease[T.normal]:cell_type[T.endothelial cell of lymphatic vessel]</th>\n",
       "      <th>disease[T.normal]:cell_type[T.endothelial cell of vascular tree]</th>\n",
       "      <th>disease[T.normal]:cell_type[T.fibroblast]</th>\n",
       "      <th>disease[T.normal]:cell_type[T.luminal epithelial cell of mammary gland]</th>\n",
       "      <th>disease[T.normal]:cell_type[T.mast cell]</th>\n",
       "      <th>disease[T.normal]:cell_type[T.myeloid cell]</th>\n",
       "      <th>disease[T.normal]:cell_type[T.pericyte]</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>P01_T cell</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P12_T cell</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P133_T cell</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P134_T cell</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P135_T cell</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P38_pericyte</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P39_pericyte</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P40_pericyte</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P41_pericyte</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>P59_pericyte</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>183 rows × 20 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              Intercept  cell_type[T.adipocyte of breast]  \\\n",
       "P01_T cell          1.0                                 0   \n",
       "P12_T cell          1.0                                 0   \n",
       "P133_T cell         1.0                                 0   \n",
       "P134_T cell         1.0                                 0   \n",
       "P135_T cell         1.0                                 0   \n",
       "...                 ...                               ...   \n",
       "P38_pericyte        1.0                                 0   \n",
       "P39_pericyte        1.0                                 0   \n",
       "P40_pericyte        1.0                                 0   \n",
       "P41_pericyte        1.0                                 0   \n",
       "P59_pericyte        1.0                                 0   \n",
       "\n",
       "              cell_type[T.basal cell]  \\\n",
       "P01_T cell                          0   \n",
       "P12_T cell                          0   \n",
       "P133_T cell                         0   \n",
       "P134_T cell                         0   \n",
       "P135_T cell                         0   \n",
       "...                               ...   \n",
       "P38_pericyte                        0   \n",
       "P39_pericyte                        0   \n",
       "P40_pericyte                        0   \n",
       "P41_pericyte                        0   \n",
       "P59_pericyte                        0   \n",
       "\n",
       "              cell_type[T.endothelial cell of lymphatic vessel]  \\\n",
       "P01_T cell                                                    0   \n",
       "P12_T cell                                                    0   \n",
       "P133_T cell                                                   0   \n",
       "P134_T cell                                                   0   \n",
       "P135_T cell                                                   0   \n",
       "...                                                         ...   \n",
       "P38_pericyte                                                  0   \n",
       "P39_pericyte                                                  0   \n",
       "P40_pericyte                                                  0   \n",
       "P41_pericyte                                                  0   \n",
       "P59_pericyte                                                  0   \n",
       "\n",
       "              cell_type[T.endothelial cell of vascular tree]  \\\n",
       "P01_T cell                                                 0   \n",
       "P12_T cell                                                 0   \n",
       "P133_T cell                                                0   \n",
       "P134_T cell                                                0   \n",
       "P135_T cell                                                0   \n",
       "...                                                      ...   \n",
       "P38_pericyte                                               0   \n",
       "P39_pericyte                                               0   \n",
       "P40_pericyte                                               0   \n",
       "P41_pericyte                                               0   \n",
       "P59_pericyte                                               0   \n",
       "\n",
       "              cell_type[T.fibroblast]  \\\n",
       "P01_T cell                          0   \n",
       "P12_T cell                          0   \n",
       "P133_T cell                         0   \n",
       "P134_T cell                         0   \n",
       "P135_T cell                         0   \n",
       "...                               ...   \n",
       "P38_pericyte                        0   \n",
       "P39_pericyte                        0   \n",
       "P40_pericyte                        0   \n",
       "P41_pericyte                        0   \n",
       "P59_pericyte                        0   \n",
       "\n",
       "              cell_type[T.luminal epithelial cell of mammary gland]  \\\n",
       "P01_T cell                                                    0       \n",
       "P12_T cell                                                    0       \n",
       "P133_T cell                                                   0       \n",
       "P134_T cell                                                   0       \n",
       "P135_T cell                                                   0       \n",
       "...                                                         ...       \n",
       "P38_pericyte                                                  0       \n",
       "P39_pericyte                                                  0       \n",
       "P40_pericyte                                                  0       \n",
       "P41_pericyte                                                  0       \n",
       "P59_pericyte                                                  0       \n",
       "\n",
       "              cell_type[T.mast cell]  cell_type[T.myeloid cell]  \\\n",
       "P01_T cell                         0                          0   \n",
       "P12_T cell                         0                          0   \n",
       "P133_T cell                        0                          0   \n",
       "P134_T cell                        0                          0   \n",
       "P135_T cell                        0                          0   \n",
       "...                              ...                        ...   \n",
       "P38_pericyte                       0                          0   \n",
       "P39_pericyte                       0                          0   \n",
       "P40_pericyte                       0                          0   \n",
       "P41_pericyte                       0                          0   \n",
       "P59_pericyte                       0                          0   \n",
       "\n",
       "              cell_type[T.pericyte]  disease[T.normal]:cell_type[T.T cell]  \\\n",
       "P01_T cell                        0                                      0   \n",
       "P12_T cell                        0                                      1   \n",
       "P133_T cell                       0                                      0   \n",
       "P134_T cell                       0                                      1   \n",
       "P135_T cell                       0                                      1   \n",
       "...                             ...                                    ...   \n",
       "P38_pericyte                      1                                      0   \n",
       "P39_pericyte                      1                                      0   \n",
       "P40_pericyte                      1                                      0   \n",
       "P41_pericyte                      1                                      0   \n",
       "P59_pericyte                      1                                      0   \n",
       "\n",
       "              disease[T.normal]:cell_type[T.adipocyte of breast]  \\\n",
       "P01_T cell                                                    0    \n",
       "P12_T cell                                                    0    \n",
       "P133_T cell                                                   0    \n",
       "P134_T cell                                                   0    \n",
       "P135_T cell                                                   0    \n",
       "...                                                         ...    \n",
       "P38_pericyte                                                  0    \n",
       "P39_pericyte                                                  0    \n",
       "P40_pericyte                                                  0    \n",
       "P41_pericyte                                                  0    \n",
       "P59_pericyte                                                  0    \n",
       "\n",
       "              disease[T.normal]:cell_type[T.basal cell]  \\\n",
       "P01_T cell                                            0   \n",
       "P12_T cell                                            0   \n",
       "P133_T cell                                           0   \n",
       "P134_T cell                                           0   \n",
       "P135_T cell                                           0   \n",
       "...                                                 ...   \n",
       "P38_pericyte                                          0   \n",
       "P39_pericyte                                          0   \n",
       "P40_pericyte                                          0   \n",
       "P41_pericyte                                          0   \n",
       "P59_pericyte                                          0   \n",
       "\n",
       "              disease[T.normal]:cell_type[T.endothelial cell of lymphatic vessel]  \\\n",
       "P01_T cell                                                    0                     \n",
       "P12_T cell                                                    0                     \n",
       "P133_T cell                                                   0                     \n",
       "P134_T cell                                                   0                     \n",
       "P135_T cell                                                   0                     \n",
       "...                                                         ...                     \n",
       "P38_pericyte                                                  0                     \n",
       "P39_pericyte                                                  0                     \n",
       "P40_pericyte                                                  0                     \n",
       "P41_pericyte                                                  0                     \n",
       "P59_pericyte                                                  0                     \n",
       "\n",
       "              disease[T.normal]:cell_type[T.endothelial cell of vascular tree]  \\\n",
       "P01_T cell                                                    0                  \n",
       "P12_T cell                                                    0                  \n",
       "P133_T cell                                                   0                  \n",
       "P134_T cell                                                   0                  \n",
       "P135_T cell                                                   0                  \n",
       "...                                                         ...                  \n",
       "P38_pericyte                                                  0                  \n",
       "P39_pericyte                                                  0                  \n",
       "P40_pericyte                                                  0                  \n",
       "P41_pericyte                                                  0                  \n",
       "P59_pericyte                                                  0                  \n",
       "\n",
       "              disease[T.normal]:cell_type[T.fibroblast]  \\\n",
       "P01_T cell                                            0   \n",
       "P12_T cell                                            0   \n",
       "P133_T cell                                           0   \n",
       "P134_T cell                                           0   \n",
       "P135_T cell                                           0   \n",
       "...                                                 ...   \n",
       "P38_pericyte                                          0   \n",
       "P39_pericyte                                          0   \n",
       "P40_pericyte                                          0   \n",
       "P41_pericyte                                          0   \n",
       "P59_pericyte                                          0   \n",
       "\n",
       "              disease[T.normal]:cell_type[T.luminal epithelial cell of mammary gland]  \\\n",
       "P01_T cell                                                    0                         \n",
       "P12_T cell                                                    0                         \n",
       "P133_T cell                                                   0                         \n",
       "P134_T cell                                                   0                         \n",
       "P135_T cell                                                   0                         \n",
       "...                                                         ...                         \n",
       "P38_pericyte                                                  0                         \n",
       "P39_pericyte                                                  0                         \n",
       "P40_pericyte                                                  0                         \n",
       "P41_pericyte                                                  0                         \n",
       "P59_pericyte                                                  0                         \n",
       "\n",
       "              disease[T.normal]:cell_type[T.mast cell]  \\\n",
       "P01_T cell                                           0   \n",
       "P12_T cell                                           0   \n",
       "P133_T cell                                          0   \n",
       "P134_T cell                                          0   \n",
       "P135_T cell                                          0   \n",
       "...                                                ...   \n",
       "P38_pericyte                                         0   \n",
       "P39_pericyte                                         0   \n",
       "P40_pericyte                                         0   \n",
       "P41_pericyte                                         0   \n",
       "P59_pericyte                                         0   \n",
       "\n",
       "              disease[T.normal]:cell_type[T.myeloid cell]  \\\n",
       "P01_T cell                                              0   \n",
       "P12_T cell                                              0   \n",
       "P133_T cell                                             0   \n",
       "P134_T cell                                             0   \n",
       "P135_T cell                                             0   \n",
       "...                                                   ...   \n",
       "P38_pericyte                                            0   \n",
       "P39_pericyte                                            0   \n",
       "P40_pericyte                                            0   \n",
       "P41_pericyte                                            0   \n",
       "P59_pericyte                                            0   \n",
       "\n",
       "              disease[T.normal]:cell_type[T.pericyte]  \n",
       "P01_T cell                                          0  \n",
       "P12_T cell                                          0  \n",
       "P133_T cell                                         0  \n",
       "P134_T cell                                         0  \n",
       "P135_T cell                                         0  \n",
       "...                                               ...  \n",
       "P38_pericyte                                        1  \n",
       "P39_pericyte                                        1  \n",
       "P40_pericyte                                        1  \n",
       "P41_pericyte                                        1  \n",
       "P59_pericyte                                        1  \n",
       "\n",
       "[183 rows x 20 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "mod.design"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "ename": "TypeError",
     "evalue": "BaseMethod.test_contrasts() takes 2 positional arguments but 3 were given",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
      "\u001b[1;32m/Users/wojciechlason/GitHub/multi-condition-comparisons/multi-condition-comparisions/docs/notebooks/example.ipynb Cell 11\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> <a href='vscode-notebook-cell:/Users/wojciechlason/GitHub/multi-condition-comparisons/multi-condition-comparisions/docs/notebooks/example.ipynb#X12sZmlsZQ%3D%3D?line=0'>1</a>\u001b[0m mod\u001b[39m.\u001b[39;49mtest_contrasts({\u001b[39m\"\u001b[39;49m\u001b[39mT cells\u001b[39;49m\u001b[39m\"\u001b[39;49m: mod\u001b[39m.\u001b[39;49mcond(disease\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mbreast cancer\u001b[39;49m\u001b[39m\"\u001b[39;49m, cell_type\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mT cell\u001b[39;49m\u001b[39m\"\u001b[39;49m) \u001b[39m-\u001b[39;49m mod\u001b[39m.\u001b[39;49mcond(disease\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mnormal\u001b[39;49m\u001b[39m\"\u001b[39;49m, cell_type\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mT cell\u001b[39;49m\u001b[39m\"\u001b[39;49m)},\n\u001b[1;32m      <a href='vscode-notebook-cell:/Users/wojciechlason/GitHub/multi-condition-comparisons/multi-condition-comparisions/docs/notebooks/example.ipynb#X12sZmlsZQ%3D%3D?line=1'>2</a>\u001b[0m                    {\u001b[39m\"\u001b[39;49m\u001b[39mfibroblasts\u001b[39;49m\u001b[39m\"\u001b[39;49m: mod\u001b[39m.\u001b[39;49mcond(disease\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mbreast cancer\u001b[39;49m\u001b[39m\"\u001b[39;49m, cell_type\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mfibroblast\u001b[39;49m\u001b[39m\"\u001b[39;49m) \u001b[39m-\u001b[39;49m mod\u001b[39m.\u001b[39;49mcond(disease\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mnormal\u001b[39;49m\u001b[39m\"\u001b[39;49m, cell_type\u001b[39m=\u001b[39;49m\u001b[39m\"\u001b[39;49m\u001b[39mfibroblast\u001b[39;49m\u001b[39m\"\u001b[39;49m)})\n",
      "\u001b[0;31mTypeError\u001b[0m: BaseMethod.test_contrasts() takes 2 positional arguments but 3 were given"
     ]
    }
   ],
   "source": [
    "mod.test_contrasts(\n",
    "    {\"T cells\": mod.cond(disease=\"breast cancer\", cell_type=\"T cell\") - mod.cond(disease=\"normal\", cell_type=\"T cell\")},\n",
    "    {\n",
    "        \"fibroblasts\": mod.cond(disease=\"breast cancer\", cell_type=\"fibroblast\")\n",
    "        - mod.cond(disease=\"normal\", cell_type=\"fibroblast\")\n",
    "    },\n",
    ")"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3.9.12 ('squidpy39')",
   "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": "3.10.13"
  },
  "vscode": {
   "interpreter": {
    "hash": "ae6466e8d4f517858789b5c9e8f0ed238fb8964458a36305fca7bddc149e9c64"
   }
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}