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  {
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   "source": [
    "# Format Conversion"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "106316f4",
   "metadata": {},
   "source": [
    "This section introduces how to do format conversion, so that you can work with other spatial tools while using Stereopy.\n",
    "\n",
    "<div class=\"alert alert-info\">\n",
    "\n",
    "**Note**\n",
    "\n",
    "Now we can add image information to the converted AnnData object, refer to [API](../content/stereo.io.stereo_to_anndata.html) for more details.\n",
    "\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4dd89129",
   "metadata": {},
   "source": [
    "## Working with Scanpy"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "id": "90f184f0",
   "metadata": {},
   "source": [
    "IO module provides the function `stereo.io.stereo_to_anndata` to convert StereoExpData object into AnnData and output the corresponding `.h5ad` file."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "54a8af2f",
   "metadata": {},
   "outputs": [],
   "source": [
    "import stereo as st\n",
    "import warnings\n",
    "warnings.filterwarnings('ignore')\n",
    "\n",
    "# read the GEF file\n",
    "data_path = './SS200000135TL_D1.tissue.gef'\n",
    "data = st.io.read_gef(file_path=data_path, bin_size=50)\n",
    "data.tl.raw_checkpoint()\n",
    "\n",
    "# remember to set flavor as scanpy \n",
    "adata = st.io.stereo_to_anndata(data,flavor='scanpy',output='scanpy_out.h5ad')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9d242f95",
   "metadata": {},
   "source": [
    "## Working with Seurat"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "id": "1fe92781",
   "metadata": {},
   "source": [
    "If you want to get the normalizetion result and convert the output `.h5ad` into the `.rds` file, you need to save raw data before performing normalization. Otherwise, it will raise errors during conversion. Conversion process mainly includes two steps."
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "id": "4dac3bf4",
   "metadata": {},
   "source": [
    "### Ouput H5ad"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "281eac2a",
   "metadata": {},
   "outputs": [],
   "source": [
    "import stereo as st\n",
    "import warnings\n",
    "warnings.filterwarnings('ignore')\n",
    "\n",
    "# read the GEF file\n",
    "data_path = './SS200000135TL_D1.tissue.gef'\n",
    "data = st.io.read_gef(file_path=data_path, bin_size=50)\n",
    "data.tl.cal_qc()\n",
    "data.tl.raw_checkpoint()\n",
    "\n",
    "# remember to set flavor as seurat \n",
    "adata = st.io.stereo_to_anndata(data,flavor='seurat',output='seurat_out.h5ad')"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "id": "aac977b9",
   "metadata": {},
   "source": [
    "### H5ad to RDS"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "id": "8459f063",
   "metadata": {},
   "source": [
    "The output `.h5ad` could be converted into `.rds` file by [h5ad2rds.R](https://github.com/STOmics/Stereopy/blob/main/docs/source/_static/h5ad2rds.R). \n",
    "\n",
    "<div class=\"alert alert-info\">\n",
    "\n",
    "**Note**\n",
    "\n",
    "The image information will be automatically added to the converted RDS file if the input h5ad file which is converted by using `st.io.stereo_to_anndata` contains the image information.\n",
    "\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c223b8c8",
   "metadata": {},
   "source": [
    "Run this command line in your own R environment:\n",
    "\n",
    "    Rscript h5ad2rds.R --infile <h5ad file> --outfile <rds file>\n",
    "\n",
    "If your own R enviroment fails to run the **h5ad2rds.R**, you can use [r-env-linux.yml](https://github.com/STOmics/Stereopy/blob/main/docs/source/_static/r-env-linux.yml) or [r-env-win.yml](https://github.com/STOmics/Stereopy/blob/main/docs/source/_static/r-env-win.yml) to create a new enviroment:\n",
    "\n",
    "    Linux: conda env create -n r-env -f r-env-linux.yml\n",
    "\n",
    "    Windows: conda env create -n r-env -f r-env-win.yml\n",
    "\n",
    "Then you need to switch to the new enviroment, start **R** and run the following command to install **seurat-disk**:\n",
    "\n",
    "    remotes::install_github(\"mojaveazure/seurat-disk\", upgrade=\"never\")\n",
    "\n",
    "In addition, you also need to install **rhdf5** in windows:\n",
    "    \n",
    "    BiocManager::install(\"rhdf5\", update=FALSE, ask=FALSE)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fe2e621c",
   "metadata": {},
   "source": []
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