{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "f9a5e963",
   "metadata": {},
   "source": [
    "# S2. Interoperability"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a0420f40",
   "metadata": {},
   "source": [
    "Here, we briefly demonstrate how the single-cell objects may be converted between R and python to run CCC analyses in either language:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "5fc40519",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import scanpy as sc\n",
    "\n",
    "data_path = '../../data/'"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "881e5514",
   "metadata": {},
   "source": [
    "## to R\n",
    "\n",
    "For use in R, the .h5ad file saved in [Tutorial 1](./01-Preprocess-Expression.ipynb) can be loaded in R as a SeuratObject using SeuratDisk. See the [companion supplementary R tutorial](../ccc_R/S2_Interoperability.ipynb) for loading these saved files.\n",
    "\n",
    "## from R\n",
    "\n",
    "### SCE\n",
    "Here, we can load the data that was generated in the [R version of Tutorial l](../ccc_R/01-Preprocess-Expression.ipynb) using SingleCellExperiment:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "b4bf8e56",
   "metadata": {},
   "outputs": [],
   "source": [
    "file_name = os.path.join(data_path, 'processed_fromR_toPython.h5ad')\n",
    "adata_fromR_sce = sc.read_h5ad(file_name)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "93014a25",
   "metadata": {},
   "source": [
    "### Seurat\n",
    "We can also load the Seurat data we generated in the [supplementary R Tutorial](../ccc_R/S0_Preprocess_Expression_Seurat.ipynb):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "7b381ded",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/hratch/miniconda3/envs/ccc_protocols/lib/python3.10/site-packages/anndata/compat/__init__.py:298: FutureWarning: Moving element from .uns['neighbors']['distances'] to .obsp['distances'].\n",
      "\n",
      "This is where adjacency matrices should go now.\n",
      "  warn(\n"
     ]
    }
   ],
   "source": [
    "file_name = os.path.join(data_path, 'processed_fromR_toPython_Seurat.h5ad')\n",
    "adata_fromR_seurat = sc.read_h5ad(file_name)"
   ]
  }
 ],
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  "language_info": {
   "codemirror_mode": {
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