Closed ixxmu closed 2 hours ago
import numpy as np
import pandas as pd
import anndata as ad
import scanpy as sc
import squidpy as sq
####读取数据
adata = sc.read_visium('/HD_data/breast_HD/binned_outputs/square_016um')
adata
AnnData object with n_obs × n_vars = 119082 × 18085
obs: 'in_tissue', 'array_row', 'array_col'
var: 'gene_ids', 'feature_types', 'genome'
uns: 'spatial'
obsm: 'spatial'
sc.pp.normalize_total(adata, inplace=True)
sc.pp.log1p(adata)
sc.pp.highly_variable_genes(adata, flavor="seurat", n_top_genes=2000)
sc.pp.scale(adata)
sc.pp.pca(adata)
sc.pp.neighbors(adata)
sc.tl.umap(adata)
sc.tl.leiden(adata, key_added="clusters", flavor="igraph", directed=False, n_iterations=2,resolution = 0.5 )
sc.pl.spatial(adata, img_key="hires", color="clusters")
https://mp.weixin.qq.com/s/lwyt_MiqQGrLNslQm8y9hA