{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "93035d74",
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"import scanpy as sc\n",
"import ToppCellPy as tp\n",
"import warnings\n",
"warnings.filterwarnings(\"ignore\")"
]
},
{
"cell_type": "markdown",
"id": "d1e40555",
"metadata": {},
"source": [
"### 1. load data"
]
},
{
"cell_type": "markdown",
"id": "23ed8540",
"metadata": {},
"source": [
"This PBMC dataset is from [Kang et al.2017](https://www.nature.com/articles/nbt.4042?report=reader), which includes two conditions (IFN stimulation and control) and six cell types. It can be downloaded from GSE96583."
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "f2fdf46b",
"metadata": {},
"outputs": [],
"source": [
"output_dir = \"/Users/jinmr2/Dropbox/Code/data/toppcell_test/\" # define output folder\n",
"adata = sc.read(\"/Users/jinmr2/Dropbox/Code/data/batch2_all_normalized_filtered.h5ad\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "c363f6df",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"AnnData object with n_obs × n_vars = 24673 × 35635\n",
" obs: 'tsne1', 'tsne2', 'ind', 'stim', 'cluster', 'cell', 'multiplets'\n",
" var: 'gene symbol'\n",
" uns: 'log1p'"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"adata"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "aae0c5d1",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"\n",
"
\n",
" \n",
" \n",
" | \n",
" tsne1 | \n",
" tsne2 | \n",
" ind | \n",
" stim | \n",
" cluster | \n",
" cell | \n",
" multiplets | \n",
"
\n",
" \n",
" \n",
" \n",
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" -27.640373 | \n",
" 14.966629 | \n",
" 1016 | \n",
" ctrl | \n",
" 9 | \n",
" CD14+ Monocytes | \n",
" singlet | \n",
"
\n",
" \n",
" | AAACATACCAGAAA-1 | \n",
" -27.493646 | \n",
" 28.924885 | \n",
" 1256 | \n",
" ctrl | \n",
" 9 | \n",
" CD14+ Monocytes | \n",
" singlet | \n",
"
\n",
" \n",
" | AAACATACCATGCA-1 | \n",
" -10.468194 | \n",
" -5.984389 | \n",
" 1488 | \n",
" ctrl | \n",
" 3 | \n",
" CD4 T cells | \n",
" singlet | \n",
"
\n",
" \n",
" | AAACATACCTCGCT-1 | \n",
" -24.367997 | \n",
" 20.429285 | \n",
" 1256 | \n",
" ctrl | \n",
" 9 | \n",
" CD14+ Monocytes | \n",
" singlet | \n",
"
\n",
" \n",
" | AAACATACCTGGTA-1 | \n",
" 27.952170 | \n",
" 24.159738 | \n",
" 1039 | \n",
" ctrl | \n",
" 4 | \n",
" Dendritic cells | \n",
" singlet | \n",
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\n",
" \n",
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"