TCGA_ChromSNV.ipynb

{
 "cells": [
  {
   "cell_type": "raw",
   "metadata": {},
   "source": [
    "---\n",
    "title: Cohort Genomics\n",
    "weight: 64\n",
    "authors:\n",
    "- kellrott\n",
    "- adamstruck\n",
    "tags:\n",
    "- tcga\n",
    "- genomics\n",
    "created_at: 2019-07-26\n",
    "updated_at: 2020-01-14\n",
    "tldr: Count the number of mutations per chromosome in the TCGA-BRCA cohort\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Connect to BMEG server"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import matplotlib.pyplot as plt\n",
    "import gripql\n",
    "conn = gripql.Connection(\"https://bmeg.io/api\", credential_file=\"bmeg_credentials.json\")\n",
    "G = conn.graph(\"rc5\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Do a query that starts on the TCGA BRCA cohort, goes though Cases -> Samples -> Aliquots -> SomaticCallsets -> Alleles.\n",
    "Once at the alleles, do an aggrigation to count the number of times each chromsome occurs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[INFO]\t2020-01-14 14:24:22,453\t1 results received in 9 seconds\n"
     ]
    }
   ],
   "source": [
    "q = G.query().V(\"Project:TCGA-BRCA\").out(\"cases\").out(\"samples\")\n",
    "q = q.has(gripql.eq(\"gdc_attributes.sample_type\", \"Primary Tumor\"))\n",
    "q = q.out(\"aliquots\").out(\"somatic_callsets\").out(\"alleles\")\n",
    "q = q.has(gripql.eq(\"variant_type\", \"SNP\"))\n",
    "q = q.aggregate(gripql.term(\"chrom\", \"chromosome\"))\n",
    "res = q.execute()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Visualize the results"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<BarContainer object of 24 artists>"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    },
    {
     "data": {
      "image/png": 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\n",
      "text/plain": [
       "<Figure size 432x288 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "name = []\n",
    "count = []\n",
    "for i in res[0].chrom.buckets:\n",
    "    name.append(i[\"key\"])\n",
    "    count.append(i[\"value\"])\n",
    "plt.bar(name, count, width=0.35)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "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": "3.7.6"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}