{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Pathway perturbation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/mnt/md0/yumin/UNAGI_old/src/perturbation_general.py:39: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual.\n",
      "  adata.obs['leiden'] = adata.obs['leiden'].astype('string')\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/mnt/md0/yumin/UNAGI_old/src/perturbation_general.py:39: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual.\n",
      "  adata.obs['leiden'] = adata.obs['leiden'].astype('string')\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/mnt/md0/yumin/UNAGI_old/src/perturbation_general.py:39: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual.\n",
      "  adata.obs['leiden'] = adata.obs['leiden'].astype('string')\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/mnt/md0/yumin/UNAGI_old/src/perturbation_general.py:39: ImplicitModificationWarning: Trying to modify attribute `.obs` of view, initializing view as actual.\n",
      "  adata.obs['leiden'] = adata.obs['leiden'].astype('string')\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n",
      "/home/yumin/anaconda3/envs/wks/lib/python3.9/site-packages/anndata/_core/anndata.py:1118: FutureWarning: is_categorical_dtype is deprecated and will be removed in a future version. Use isinstance(dtype, CategoricalDtype) instead\n",
      "  if not is_categorical_dtype(df_full[k]):\n"
     ]
    }
   ],
   "source": [
    "#pathway perturbation results\n",
    "import scanpy as sc\n",
    "import numpy as np\n",
    "import pickle\n",
    "from UNAGI.speedup_perturbation import perturbation\n",
    "adata = sc.read_h5ad('dataset.h5ad')\n",
    "uns = pickle.load(open('attribute.pkl', 'rb'))\n",
    "keys = list(uns['random_background_perturbation_deltaD']['0.5'].keys()).copy()\n",
    "del uns['random_background_perturbation_deltaD']['0.5']\n",
    "del uns['random_background_perturbation_deltaD']['2.0']\n",
    "del uns['pathway_perturbation_score']\n",
    "\n",
    "adata.uns = uns\n",
    "#pathway median gene len: 4\n",
    "#pathway mean gene len: 8\n",
    "a = perturbation(adata, 'model_save/mes_4.pth','idrem')\n",
    "\n",
    "\n",
    "a.run('random_background',0.5,random_genes=20,random_times=1000,inplace=True)\n",
    "a.run('pathway',0.5,inplace=True)\n",
    "a.analysis('pathway',0.5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "pd.DataFrame.from_dict(adata.uns['pathway_perturbation_score']['0.5']['total']['top_pathways']).to_csv('pathway_results.csv')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Drug perturbation"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#drug perturbation results\n",
    "import scanpy as sc\n",
    "import numpy as np\n",
    "import pickle\n",
    "from UNAGI.speedup_perturbation import perturbation\n",
    "adata = sc.read_h5ad('dataset.h5ad')\n",
    "uns = pickle.load(open('attribute.pkl', 'rb'))\n",
    "keys = list(uns['random_background_perturbation_deltaD']['0.5'].keys()).copy()\n",
    "del uns['random_background_perturbation_deltaD']['0.5']\n",
    "del uns['random_background_perturbation_deltaD']['2.0']\n",
    "del uns['pathway_perturbation_score']\n",
    "\n",
    "adata.uns = uns\n",
    "#drug median gene len: 2\n",
    "#drug mean gene len: 2\n",
    "a = perturbation(adata, 'model_save/mes_4.pth','idrem')\n",
    "\n",
    "a.run('random_background',0.5,random_genes=20,random_times=1000,inplace=True)\n",
    "a.run('drug',0.5,inplace=True)\n",
    "a.analysis('drug',0.5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "pd.DataFrame.from_dict(adata.uns['drug_perturbation_score']['0.5']['total']['top_compounds']).to_csv('drug_results.csv')"
   ]
  }
 ],
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