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hi
i run hotspot like this
import scanpy as sc import anndata as ad import pandas as pd import hotspot import numpy as np import mplscience import matplotlib import sys infile = sys.argv[1] adata = sc.read_h5ad(infile) adata.obs_names_make_unique() adata.var_names_make_unique() sc.pp.filter_genes(adata, min_cells=3) adata.obs["total_counts"] = np.asarray(adata.X.sum(1)).ravel() adata.layers["csc_counts"] = adata.X.tocsc() sc.pp.normalize_total(adata) sc.pp.log1p(adata) # step1 Create the Hotspot object and the neighborhood graph hs = hotspot.Hotspot( adata, layer_key="csc_counts", model='bernoulli', latent_obsm_key="spatial", umi_counts_obs_key="total_counts", ) hs.create_knn_graph( weighted_graph=False, n_neighbors=300, ) # step2 hs_results = hs.compute_autocorrelations() ## step3: hs_genes = hs_results.index[hs_results.FDR < 0.05] lcz = hs.compute_local_correlations(hs_genes) modules = hs.create_modules( min_gene_threshold=20, core_only=False, fdr_threshold=0.05 ) ## step4: import pickle with open('test.pkl', 'wb') as f: pickle.dump(hs, f) ## read hotspot pkl with open('hotspot.C1.pkl', 'rb') as f: hss = pickle.load(f) hss.plot_local_correlations() # get output hss.results # get output hss.modules # get output hss.local_correlation_z # get output hss.module_scores # return nothing
can you help me resolve the problem. thanks.
The text was updated successfully, but these errors were encountered:
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hi
i run hotspot like this
can you help me resolve the problem.
thanks.
The text was updated successfully, but these errors were encountered: