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{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"id": "e10ac0c9-40ce-41fb-b6fa-3d62b76f2e57",
"metadata": {},
"outputs": [],
"source": [
"from geneformer import InSilicoPerturber\n",
"from geneformer import InSilicoPerturberStats"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "67b44366-f255-4415-a865-6a27a8ffcce7",
"metadata": {
"tags": []
},
"outputs": [],
"source": [
"# in silico perturbation in deletion mode to determine genes whose \n",
"# deletion in the dilated cardiomyopathy (dcm) state significantly shifts\n",
"# the embedding towards non-failing (nf) state\n",
"isp = InSilicoPerturber(perturb_type=\"delete\",\n",
" perturb_rank_shift=None,\n",
" genes_to_perturb=\"all\",\n",
" combos=0,\n",
" anchor_gene=None,\n",
" model_type=\"CellClassifier\",\n",
" num_classes=3,\n",
" emb_mode=\"cell\",\n",
" cell_emb_style=\"mean_pool\",\n",
" filter_data={\"cell_type\":[\"Cardiomyocyte1\",\"Cardiomyocyte2\",\"Cardiomyocyte3\"]},\n",
" cell_states_to_model={'state_key': 'disease', \n",
" 'start_state': 'dcm', \n",
" 'goal_state': 'nf', \n",
" 'alt_states': ['hcm']},\n",
" max_ncells=2000,\n",
" emb_layer=0,\n",
" forward_batch_size=400,\n",
" nproc=16)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0525a663-871a-4ce0-a135-cc203817ffa9",
"metadata": {},
"outputs": [],
"source": [
"# outputs intermediate files from in silico perturbation\n",
"isp.perturb_data(\"path/to/model\",\n",
" \"path/to/input_data\",\n",
" \"path/to/output_directory\",\n",
" \"output_prefix\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f8aadabb-516a-4dc0-b307-6de880e64e26",
"metadata": {},
"outputs": [],
"source": [
"ispstats = InSilicoPerturberStats(mode=\"goal_state_shift\",\n",
" genes_perturbed=\"all\",\n",
" combos=0,\n",
" anchor_gene=None,\n",
" cell_states_to_model={\"disease\":([\"dcm\"],[\"nf\"],[\"hcm\"])})"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ffecfae6-e737-43e3-99e9-fa37ff46610b",
"metadata": {},
"outputs": [],
"source": [
"# extracts data from intermediate files and processes stats to output in final .csv\n",
"ispstats.get_stats(\"path/to/input_data\",\n",
" None,\n",
" \"path/to/output_directory\",\n",
" \"output_prefix\")"
]
}
],
"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": "3.10.11"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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