{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### custom signatures and ssGSEA method"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "from GSVA import gmt_to_dataframe\n",
    "import gseapy as gp"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Gene Symbols Conversion for the GMT file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "custom_signatures = gmt_to_dataframe(\"tests/extdata/enrichr.KEGG_2016.gmt\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### ssGSEA method\n",
    "ref: https://gseapy.readthedocs.io/en/latest/singlecell_example.html"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "res = gp.gsea(data=adata.to_df().T, # row -> genes, column-> samples\n",
    "        gene_sets=\"tests/extdata/enrichr.KEGG_2016.gmt\",\n",
    "        cls=adata.obs.stim,\n",
    "        permutation_num=1000,\n",
    "        permutation_type='phenotype',\n",
    "        outdir=None,\n",
    "        method='s2n', # signal_to_noise\n",
    "        threads= 16)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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