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updated viz
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@srivarra
srivarra committed May 1, 2024
1 parent c9c6047 commit 1974915
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Showing 26 changed files with 109 additions and 57 deletions.
6 changes: 3 additions & 3 deletions data/embedded_data.zarr/X/.zarray
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4 changes: 2 additions & 2 deletions data/embedded_data.zarr/var/$PnB/.zarray
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4 changes: 2 additions & 2 deletions data/embedded_data.zarr/var/$PnE/codes/.zarray
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4 changes: 2 additions & 2 deletions data/embedded_data.zarr/var/$PnR/codes/.zarray
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4 changes: 2 additions & 2 deletions data/embedded_data.zarr/var/_index/.zarray
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4 changes: 2 additions & 2 deletions data/embedded_data.zarr/var/channel/categories/.zarray
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4 changes: 2 additions & 2 deletions data/embedded_data.zarr/var/channel/codes/.zarray
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4 changes: 2 additions & 2 deletions data/embedded_data.zarr/var/marker/categories/.zarray
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4 changes: 2 additions & 2 deletions data/embedded_data.zarr/var/marker/codes/.zarray
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4 changes: 2 additions & 2 deletions data/embedded_data.zarr/var/n/categories/.zarray
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4 changes: 2 additions & 2 deletions data/embedded_data.zarr/var/n/codes/.zarray
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69 changes: 56 additions & 13 deletions scripts/process_fcs.ipynb
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},
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"cell_type": "code",
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"cell_type": "code",
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"execution_count": null,
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"cell_type": "code",
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},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": null,
"metadata": {},
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"source": [
"cell_type_mapping = {0: \"Healthy\", 1: \"Healthy\", 2: \"Cancer\"}\n",
"patient_annotation = {0: \"Healthy\", 1: \"Cancer\", 2: \"Cancer\"}\n",
"cell_type_patient_mapping = {\n",
" 0: \"Healthy_Patient_Healthy_Cells\",\n",
" 1: \"Cancer_Patient_Healthy_Cells\",\n",
" 2: \"Cancer_Patient_Cancer_Cells\",\n",
" 0: \"Healthy Cells\",\n",
" 1: \"Queen Bee Cells\",\n",
" 2: \"Cancer Cells\",\n",
"}\n",
"new_adata.obs[\"cell_type\"] = new_adata.obs[\"OmiqFileIndex\"].map(cell_type_mapping).astype(\"category\")\n",
"new_adata.obs[\"patient\"] = new_adata.obs[\"OmiqFileIndex\"].map(patient_annotation).astype(\"category\")\n",
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"cell_type": "code",
"execution_count": 7,
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"cell_type": "code",
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"execution_count": null,
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},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"new_adata.write_zarr(\"../data/embedded_data.zarr\")"
"markers = [\"141Pr_pPLCg2\", \"150Sm_pSTAT5\", \"159Tb_pAkt\", \"166Er_pSyk\", \"176Yb_pCreb\"]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"new_adata2 = new_adata.copy()[:, markers]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"renamed_markers = [\"Gamma\", \"STAT5\", \"AKT\", \"SYK\", \"CREB\"]"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"new_adata2.var_names = renamed_markers"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"new_adata2.write_zarr(\"../data/embedded_data.zarr\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
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],
"metadata": {
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