define_ground_truth.ipynb

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  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "31df2906",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import scanpy as sc\n",
    "import pickle as pickle"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b7db63d4",
   "metadata": {},
   "source": [
    "Define ground truth for clusters transitions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "5ced8852",
   "metadata": {},
   "outputs": [],
   "source": [
    "HumanDevelopingBrain = [(\"Radial Glia\", \"Intermediate \\n Progenitor\"),\n",
    "                        (\"Intermediate \\n Progenitor\", \"Newborn \\n Excitatory Neuron\"),\n",
    "                        (\"Newborn \\n Excitatory Neuron\", \"Immature \\n Excitatory Neuron\"),\n",
    "                        (\"Immature \\n Excitatory Neuron\", \"Mature \\n Excitatory Neuron\")]\n",
    "HumanBoneMarrow = [(\"HSC_1\", \"Ery_1\"), (\"HSC_1\", \"HSC_2\"), (\"Ery_1\", \"Ery_2\")]\n",
    "DentateGyrus  = [('nIPC', 'Neuroblast'), ('Neuroblast', 'Granule immature'), ('Granule immature', 'Granule mature'),\n",
    "                 (\"Radial Glia-like\", \"Astrocytes\"), (\"OPC\", \"OL\")]\n",
    "Pancreas_with_cc = [(\"Ngn3 high EP\", \"Pre-endocrine\"), (\"Pre-endocrine\", \"Alpha\"), (\"Pre-endocrine\", \"Beta\"), (\"Pre-endocrine\", \"Delta\"), (\"Pre-endocrine\", \"Epsilon\")]\n",
    "MouseBoneMarrow = [('dividing', 'progenitors'), ('progenitors', 'activating')]\n",
    "MouseErythroid = [(\"Blood progenitors 1\", \"Blood progenitors 2\"), (\"Blood progenitors 2\", \"Erythroid1\"),\n",
    "                  (\"Erythroid1\", \"Erythroid2\"), (\"Erythroid2\", \"Erythroid3\")]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "25953e44",
   "metadata": {},
   "outputs": [],
   "source": [
    "save_dir = '/nfs/team283/aa16/data/fate_benchmarking/benchmarking_datasets/'\n",
    "with open(save_dir + '/HumanDevelopingBrain/HumanDevelopingBrain_groundTruth.pickle', 'wb') as handle:\n",
    "    pickle.dump(HumanDevelopingBrain, handle, protocol=pickle.HIGHEST_PROTOCOL)\n",
    "with open(save_dir + '/HumanErythroid/HumanErythroid_groundTruth.pickle', 'wb') as handle:\n",
    "    pickle.dump(HumanErythroid, handle, protocol=pickle.HIGHEST_PROTOCOL)\n",
    "with open(save_dir + '/HumanBoneMarrow/HumanBoneMarrow_groundTruth.pickle', 'wb') as handle:\n",
    "    pickle.dump(HumanBoneMarrow, handle, protocol=pickle.HIGHEST_PROTOCOL)\n",
    "with open(save_dir + '/DentateGyrus/DentateGyrus_groundTruth.pickle', 'wb') as handle:\n",
    "    pickle.dump(DentateGyrus, handle, protocol=pickle.HIGHEST_PROTOCOL)\n",
    "with open(save_dir + '/Pancreas_with_cc/Pancreas_with_cc_groundTruth.pickle', 'wb') as handle:\n",
    "    pickle.dump(Pancreas_with_cc, handle, protocol=pickle.HIGHEST_PROTOCOL)\n",
    "with open(save_dir + '/MouseErythroid/MouseErythroid_groundTruth.pickle', 'wb') as handle:\n",
    "    pickle.dump(MouseErythroid, handle, protocol=pickle.HIGHEST_PROTOCOL)\n",
    "with open(save_dir + '/MouseBoneMarrow/MouseBoneMarrow_groundTruth.pickle', 'wb') as handle:\n",
    "    pickle.dump(MouseBoneMarrow, handle, protocol=pickle.HIGHEST_PROTOCOL)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "766e796a",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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