{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Run downstream tasks to analyze the UNAGI outcomes\n",
    "\n",
    "UNAGI provides all an all-in-one solution to perform downstream to analyse its outcomes. The function `UNAGI.analyse_UNAGI` can identify the dynamic markers and hierarchical static markers, perform pathway and compound perturbations. This function takes the h5ad file generated by UNAGI and the iteration of the generated file as the inputs. Users are also required to specify the number of sampling times to build the random distribution background of dynamic markers. Users can use the precomputed CMAP dataset (download from Example data) to perform the drug perturbation. If users have a specific interest of compoound sets to user, they can customize a compound file. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from UNAGI import UNAGI\n",
    "unagi = UNAGI()\n",
    "\n",
    "generated_data = 'UNAGI_generated_data' # data generated by UNAGI\n",
    "data_iteration = NUM_ITERATION # iteration of UNAGI\n",
    "sampling_times = SAMPLING_TIMES # sampling times of UNAGI\n",
    "save_dir = 'DIRECTORY_TO_SAVE_ANALYZED_DATA' # directory to save result\n",
    "cmap_dir = 'PRECOMPUTED_CMAP_DATA' # directory to precomputed cmap data\n",
    "customized_drug = 'CUSTOMIZED_DRUG_TARGET_PAIR' # customized drug target pair if needed\n",
    "\n",
    "unagi.analyse_UNAGI(generated_data,data_iteration,sampling_times,target_dir=save_dir,customized_drug=customized_drug,cmap_dir=cmap_dir)"
   ]
  }
 ],
 "metadata": {
  "language_info": {
   "name": "python"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}