脚本更新---高精度平台的细胞niche分析

###pip install SOAPy_st
import warnings
warnings.filterwarnings("ignore")
import scanpy as sc
import SOAPy_st as sp
import numpy as np

adata = sc.read('spatial.h5ad')

sp.pp.make_network(adata, sample_key='sample', method='radius', cutoff=100, scale=1.0, cluster_key='cluster') 

sp.tl.get_c_niche(adata=adata_com, k_max=30, celltype_key='cluster', sample_key='sample')

AnnData object with n_obs × n_vars = 211649 × 44
    obs: 'sample', 'leiden', 'cluster', 'C_niche'
    var: 'highly_variable'
    uns: 'cluster_colors', 'leiden', 'leiden_colors', 'neighbors', 'pca', 'umap', 'var_for_clustering', 'SOAPy'
    obsm: 'X_pca', 'X_umap', 'spatial'
    varm: 'PCs'
    obsp: 'connectivities', 'distances'

fig = sp.pl.show_celltype_niche_heatmap(adata=adata_com, cmap = 'coolwarm', figsize=(20, 16))