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系统学习python(四)对于Scanpy的整理

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接着上文继续学习Scanpy的相关语法 ,参考网页

Preprocessing and clustering

import scanpy as sc
import anndata as ad

sc.settings.set_figure_params(dpi=50, facecolor="white")

# EXAMPLE_DATA = pooch.create(
#    path=pooch.os_cache("scverse_tutorials"),
#    base_url="doi:10.6084/m9.figshare.22716739.v1/",
# )
# EXAMPLE_DATA.load_registry_from_doi()

samples = {
    "s1d1": "D:\\articleCode\\research\\s1d1_filtered_feature_bc_matrix.h5",
    "s1d3": "D:\\articleCode\\research\\s1d3_filtered_feature_bc_matrix.h5",
}
adatas = {}

for sample_id, path in samples.items():
    sample_adata = sc.read_10x_h5(path)
    sample_adata.var_names_make_unique()
    print(sample_adata)
    adatas[sample_id] = sample_adata

adata = ad.concat(adatas, label="sample")
adata.obs_names_make_unique()
print(adata.obs["sample"].value_counts())
print(adata)