97 lines (96 with data), 2.6 kB

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import sys"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "sys.path.append('..')\n",
    "\n",
    "from pyMultiOmics.plots import download_reactome_diagram\n",
    "from pyMultiOmics.constants import HOMO_SAPIENS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "2022-03-24 14:49:06.061 | DEBUG    | pyMultiOmics.plots:send_reactome_expression_data:86 - POSTing expression data to Reactome Analysis Service: https://reactome.org/AnalysisService/identifiers/?interactors=false&species=Homo%20sapiens&sortBy=ENTITIES_PVALUE&order=ASC&resource=TOTAL&pValue=1&includeDisease=true\n",
      "2022-03-24 14:49:07.812 | DEBUG    | pyMultiOmics.plots:send_reactome_expression_data:90 - Received HTTP status code: 200\n",
      "2022-03-24 14:49:07.817 | DEBUG    | pyMultiOmics.plots:parse_reactome_json:115 - Received expression analysis token: MjAyMjAzMjQxMDIxMjdfNDExOTA%3D\n",
      "2022-03-24 14:49:08.834 | DEBUG    | pyMultiOmics.plots:download_reactome_diagram:67 - Image saved to reactome.png\n"
     ]
    }
   ],
   "source": [
    "stId = 'R-HSA-70921'\n",
    "out_file = 'reactome.png'\n",
    "exp_dict = {\n",
    "    'C00135': 1.0,           # kegg\n",
    "    'C01342': 2.0,           # kegg\n",
    "    '30817': 3.0,            # ChEBI\n",
    "    'HAL': 4.0,              # gene name\n",
    "    'ENSG00000172508': 5.0,  # ensembl\n",
    "    'Q96NU7': 6.0            # uniprot\n",
    "}\n",
    "\n",
    "download_reactome_diagram(stId, out_file, species=HOMO_SAPIENS, expression_dict=exp_dict)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "![title](reactome.png)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.1"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}