{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "a2bf98c2", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/data_nfs/og86asub/netmap/netmap-evaluation/netmap/.pixi/envs/default/lib/python3.12/site-packages/celltypist/classifier.py:11: FutureWarning: `__version__` is deprecated, use `importlib.metadata.version('scanpy')` instead\n", " from scanpy import __version__ as scv\n" ] } ], "source": [ "\n", "import anndata as ad\n", "import celltypist\n", "from celltypist import models\n", "import scanpy as sc\n", "import numpy as np" ] }, { "cell_type": "code", "execution_count": 2, "id": "e0da77e9", "metadata": {}, "outputs": [], "source": [ "np.random.seed(12)" ] }, { "cell_type": "code", "execution_count": 3, "id": "e820596e", "metadata": {}, "outputs": [], "source": [ "## Load adata (prefiltered by cellrange/rhapsody)\n", "adata = sc.read_10x_mtx('netmap/data/blood/rhapsody/rhapsody_out/')\n" ] }, { "cell_type": "code", "execution_count": 4, "id": "1e8105ae", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | gene_ids | \n", "feature_types | \n", "
|---|---|---|
| A1BG | \n", "ENSG00000121410.13 | \n", "Gene Expression | \n", "
| A1BG-AS1 | \n", "ENSG00000268895.6 | \n", "Gene Expression | \n", "
| A1CF | \n", "ENSG00000148584.17 | \n", "Gene Expression | \n", "
| A2M | \n", "ENSG00000175899.16 | \n", "Gene Expression | \n", "
| A2M-AS1 | \n", "ENSG00000245105.5 | \n", "Gene Expression | \n", "
| ... | \n", "... | \n", "... | \n", "
| ZYG11B | \n", "ENSG00000162378.14 | \n", "Gene Expression | \n", "
| ZYX | \n", "ENSG00000159840.17 | \n", "Gene Expression | \n", "
| ZZEF1 | \n", "ENSG00000074755.16 | \n", "Gene Expression | \n", "
| ZZZ3 | \n", "ENSG00000036549.14 | \n", "Gene Expression | \n", "
| hsa-mir-423 | \n", "ENSG00000266919.3 | \n", "Gene Expression | \n", "
46998 rows × 2 columns
\n", "