{"id":68832,"date":"2026-11-14T21:03:30","date_gmt":"2026-11-14T13:03:30","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=68832"},"modified":"2026-11-14T21:03:30","modified_gmt":"2026-11-14T13:03:30","slug":"squidpy-neighborhood-enrichment-radius-null-edges","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/squidpy-neighborhood-enrichment-radius-null-edges\/","title":{"rendered":"Squidpy \u8bf4\u4e24\u7c7b\u7ec6\u80de\u76f8\u90bb\u5bcc\u96c6\uff0c\u5148\u770b\u770b\u54ea\u4e24\u70b9\u7b97\u90bb\u5c45"},"content":{"rendered":"
\n

\u4e00\u5f20\u7a7a\u95f4\u56fe\u663e\u793a\u80bf\u7624\u7ec6\u80de\u4e0e\u5de8\u566c\u7ec6\u80de\u76f8\u90bb\u5bcc\u96c6\u3002\u628a\u5efa\u56fe\u534a\u5f84\u4ece\u5341\u5fae\u7c73\u8c03\u5230\u4e09\u5341\u5fae\u7c73\uff0c\u539f\u6765\u7684\u7ea2\u8272\u533a\u57df\u5374\u51e0\u4e4e\u6d88\u5931\u3002\u4e24\u7ec4\u7ed3\u679c\u672a\u5fc5\u77db\u76fe\uff0c\u5341\u5fae\u7c73\u548c\u4e09\u5341\u5fae\u7c73\u53ef\u80fd\u5728\u56de\u7b54\u4e24\u4e2a\u4e0d\u540c\u7684\u7ec4\u7ec7\u5b66\u95ee\u9898\u3002\u5224\u65ad\u4e4b\u524d\uff0c\u6700\u597d\u5148\u4ece\u771f\u5b9e\u5750\u6807\u753b\u51fa\u4e00\u5c0f\u5757\u90bb\u5c45\u8fb9\uff0c\u7b97\u6e05\u7528\u4e86\u591a\u5927\u7684\u90bb\u8fd1\u5c3a\u5ea6\uff0c\u518d\u56de\u6765\u770b\u5bcc\u96c6\u5206\u6570\u7684\u5206\u6bcd\u3002\u4e0b\u9762\u7528\u6392\u6210\u4e00\u884c\u7684\u56db\u4e2a\u70b9\uff0c\u91cd\u73b0\u4ec5\u6539\u53d8\u534a\u5f84\u5c31\u8db3\u4ee5\u6539\u53d8\u7ed3\u679c\u7684\u539f\u56e0\u3002<\/p>\n

\u5148\u51b3\u5b9a\u90bb\u8fd1\u6307\u7ec6\u80de\u63a5\u89e6\u3001\u5c40\u90e8\u5171\u5c45\u8fd8\u662f\u540c\u5904\u4e00\u4e2a\u533a\u57df<\/h2>\n

\u5728\u6210\u50cf\u6570\u636e\u91cc\uff0c\u7ec6\u80de\u8d28\u8f6e\u5ed3\u771f\u6b63\u63a5\u89e6\uff0c\u7ec6\u80de\u4e2d\u5fc3\u672a\u5fc5\u7279\u522b\u8fd1\u3002\u5927\u7ec6\u80de\u548c\u5c0f\u7ec6\u80de\u7684\u4e2d\u5fc3\u8ddd\u79bb\u6070\u597d\u4e00\u6837\uff0c\u4e5f\u53ef\u80fd\u6709\u5b8c\u5168\u4e0d\u540c\u7684\u8fb9\u754c\u5173\u7cfb\u3002\u82e5\u8981\u7814\u7a76\u63a5\u89e6\u4f9d\u8d56\u7684\u4fe1\u53f7\uff0c\u8d28\u5fc3\u534a\u5f84\u53ea\u80fd\u4f5c\u4e3a\u8fd1\u4f3c\uff0c\u6709\u8fb9\u754c\u65f6\u53ef\u8fdb\u4e00\u6b65\u6838\u5bf9\u8f6e\u5ed3\u3002\u82e5\u95ee\u9898\u662f\u67d0\u7c7b\u7ec6\u80de\u662f\u5426\u805a\u5728\u540c\u4e00\u8840\u7ba1\u5468\u56f4\uff0c\u5219\u8f83\u5927\u7684\u7269\u7406\u534a\u5f84\u53ef\u80fd\u66f4\u8d34\u8fd1\u95ee\u9898\u3002\u5148\u6839\u636e\u7ec4\u7ec7\u5c3a\u5ea6\u786e\u5b9a\u8981\u63cf\u8ff0\u4ec0\u4e48\uff0c\u540e\u9762\u6539\u53d8\u534a\u5f84\u624d\u6709\u89e3\u91ca\u5bf9\u8c61\u3002<\/p>\n

\u4ece\u7a7a\u95f4\u5bf9\u8c61\u8bfb\u53d6\u5750\u6807\u540e\u8981\u67e5\u5355\u4f4d\u3002\u56fe\u50cf\u50cf\u7d20\u548c\u5fae\u7c73\u4e4b\u95f4\u9700\u8981\u5b9e\u9645\u6821\u51c6\uff0c\u7f29\u7565\u56fe\u4e0a\u7684\u50cf\u7d20\u4e5f\u672a\u5fc5\u7b49\u4e8e\u539f\u56fe\u50cf\u7d20\u3002\u591a\u4e2a\u5207\u7247\u7ecf\u5e38\u5404\u81ea\u628a\u5de6\u4e0a\u89d2\u8bb0\u4e3a\u96f6\uff0c\u76f4\u63a5\u62fc\u63a5\u5750\u6807\u4f1a\u9020\u6210\u4e0d\u540c\u5207\u7247\u7684\u7ec6\u80de\u53d8\u6210\u8fd1\u90bb\u3002\u5efa\u56fe\u65f6\u8ba9\u6bcf\u5f20\u5207\u7247\u72ec\u7acb\uff0c\u68c0\u67e5\u6700\u7ec8\u90bb\u63a5\u77e9\u9635\u4e2d\u662f\u5426\u6709\u8de8\u5207\u7247\u8fb9\u3002\u5373\u4f7f\u5c06\u4e0d\u540c\u5207\u7247\u5728\u753b\u5e03\u4e0a\u5e73\u79fb\u5f00\uff0c\u4e5f\u5e94\u8be5\u628a\u6765\u6e90\u5b57\u6bb5\u4fdd\u5b58\u4e0b\u6765\uff0c\u4e0d\u80fd\u4f9d\u8d56\u4e00\u5f20\u4e34\u65f6\u6392\u7248\u56fe\u7684\u5750\u6807\u95f4\u8ddd\u6765\u5b9a\u4e49\u771f\u5b9e\u7ec4\u7ec7\u90bb\u5c45\u3002Squidpy \u534a\u5f84\u5efa\u56fe\u7684\u53c2\u6570\u4e0e\u8ddd\u79bb\u5b9a\u4e49<\/a><\/p>\n

\u7528\u56db\u4e2a\u70b9\u624b\u7b97\u90bb\u5c45\u8fb9\u4e0e\u968f\u673a\u57fa\u7ebf<\/h2>\n

\u8bbe\u4e00\u884c\u56db\u4e2a\u7ec6\u80de\u4e2d\u5fc3\u5206\u522b\u5728\u96f6\u3001\u5341\u3001\u4e8c\u5341\u3001\u4e09\u5341\u5fae\u7c73\u5904\uff0c\u7c7b\u578b\u4ece\u5de6\u5230\u53f3\u4e3a\u7532\u3001\u4e59\u3001\u7532\u3001\u4e59\u3002\u8bbe\u534a\u5f84\u5305\u542b\u6070\u597d\u7b49\u4e8e\u9608\u503c\u7684\u70b9\uff0c\u4e0d\u4fdd\u7559\u81ea\u73af\uff0c\u6bcf\u5bf9\u65e0\u5411\u90bb\u5c45\u53ea\u6570\u4e00\u6b21\u3002\u5341\u5fae\u7c73\u65f6\u53ea\u6709\u4e09\u5bf9\u76f8\u90bb\u4f4d\u7f6e\uff0c\u6bcf\u4e00\u5bf9\u90fd\u662f\u7532\u4e59\u3002\u4e8c\u5341\u4e00\u5fae\u7c73\u65f6\u8fd8\u4f1a\u52a0\u4e0a\u7b2c\u4e00\u4e0e\u7b2c\u4e09\u3001\u7b2c\u4e8c\u4e0e\u7b2c\u56db\u8fd9\u4e24\u5bf9\u540c\u7c7b\u7ec6\u80de\uff0c\u603b\u8fb9\u6570\u4ece\u4e09\u53d8\u6210\u4e94\uff0c\u7532\u4e59\u8fb9\u6570\u4ecd\u4e3a\u4e09\u3002<\/p>\n

\n\n\n\n\n\n\n\n
\u534a\u5f84<\/th>\n\u65e0\u5411\u8fb9\u6570<\/th>\n\u7532\u4e59\u8fb9\u6570<\/th>\n\u7532\u4e59\u8fb9\u5360\u6bd4<\/th>\n<\/tr>\n<\/thead>\n
10 \u5fae\u7c73<\/td>\n3<\/td>\n3<\/td>\n100%<\/td>\n<\/tr>\n
21 \u5fae\u7c73<\/td>\n5<\/td>\n3<\/td>\n60%<\/td>\n<\/tr>\n
31 \u5fae\u7c73<\/td>\n6<\/td>\n4<\/td>\n\u7ea6 67%<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u534a\u5f84\u4e00\u6539\uff0c\u90bb\u57df\u5bcc\u96c6\u4e3a\u4f55\u4e5f\u4f1a\u6539\u3002\u6559\u5b66\u7b97\u4f8b\uff5c\u56db\u4e2a\u7ec6\u80de\u6bcf\u9694\u5341\u5fae\u7c73\u4e00\u4e2a\uff0c\u7c7b\u578b\u4f9d\u6b21\u4e3a\u7532\u4e59\u7532\u4e59\u300210
\u6559\u5b66\u7b97\u4f8b\uff5c\u56db\u4e2a\u7ec6\u80de\u6bcf\u9694\u5341\u5fae\u7c73\u4e00\u4e2a\uff0c\u7c7b\u578b\u4f9d\u6b21\u4e3a\u7532\u4e59\u7532\u4e59\u3002<\/figcaption><\/figure>\n

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\u624b\u7b97\u7684\u662f\u65e0\u5411\u603b\u4f53\u8fb9\u3002\u8f6f\u4ef6\u8f93\u51fa\u6309\u6765\u6e90\u7c7b\u578b\u4e0e\u90bb\u5c45\u7c7b\u578b\u7ec4\u7ec7\uff0c\u67d0\u4e9b\u8bfb\u6cd5\u8fd8\u4f1a\u533a\u5206\u7532\u5230\u4e59\u4e0e\u4e59\u5230\u7532\uff0c\u4ee5\u53ca\u540c\u7c7b\u578b\u8fb9\u5728\u5bf9\u79f0\u77e9\u9635\u4e2d\u7684\u4e24\u7aef\u3002\u4f5c\u6838\u5bf9\u65f6\u59cb\u7ec8\u4fdd\u6301\u8ba1\u6570\u53e3\u5f84\u4e00\u81f4\u3002\u7f6e\u6362\u6807\u51c6\u5206\u53cd\u6620\u89c2\u6d4b\u4e0e\u7f6e\u6362\u5747\u503c\u4e4b\u95f4\u76f8\u5dee\u591a\u5c11\u4e2a\u7f6e\u6362\u6807\u51c6\u5dee\uff0c\u7edd\u4e0d\u662f\u201c\u76f8\u90bb\u6982\u7387\u4e3a\u591a\u5c11\u201d\u3002\u540c\u4e00\u4efd\u6570\u636e\u91cc\u7a00\u6709\u7fa4\u548c\u4e30\u5bcc\u7fa4\u62e5\u6709\u7684\u53ef\u7528\u8fb9\u6570\u5dee\u5f88\u591a\uff0c\u4e24\u5f20\u90fd\u4e3a\u6df1\u7ea2\u8272\u7684\u683c\u5b50\u4e5f\u53ef\u80fd\u5bf9\u5e94\u622a\u7136\u4e0d\u540c\u7684\u7edd\u5bf9\u8fb9\u6570\u3002Squidpy \u90bb\u57df\u5bcc\u96c6\u7684\u8ba1\u6570\u4e0e\u7f6e\u6362\u8f93\u51fa<\/a><\/p>\n

\u5efa\u56fe\u540e\u5148\u67e5\u6709\u6ca1\u6709\u8de8\u7247\u7684\u8fb9<\/h2>\n

\u4e0b\u4f8b\u5047\u8bbe\u6240\u7528 Squidpy \u7248\u672c\u63d0\u4f9b\u534a\u5f84\u5efa\u56fe\u63a5\u53e3\uff0c\u5750\u6807\u5df2\u6362\u4e3a\u5fae\u7c73\uff0c\u5207\u7247\u7f16\u53f7\u548c\u7c7b\u578b\u5df2\u8bbe\u4e3a\u7c7b\u522b\u5217\u3002\u793a\u8303\u534a\u5f84\u7528\u4e8c\u5341\u4e00\uff0c\u4e0e\u4e0a\u8868\u5bf9\u5e94\u3002\u90bb\u63a5\u662f\u6309\u5207\u7247\u6784\u9020\u7684\uff0c\u968f\u540e\u7edf\u8ba1\u65f6\u4ecd\u63d0\u4f9b\u5207\u7247\u7f16\u53f7\uff0c\u4ee5\u4fbf\u5728\u76f8\u5e94\u5207\u7247\u5185\u5bf9\u6807\u7b7e\u4f5c\u7f6e\u6362\u3002\u4ee3\u7801\u5148\u68c0\u67e5\u8fb9\u7684\u4e24\u4e2a\u7aef\u70b9\u662f\u5426\u771f\u7684\u6765\u81ea\u540c\u4e00\u5f20\u5207\u7247\uff0c\u518d\u8ba1\u7b97\u5bcc\u96c6\u3002<\/p>\n

import squidpy as sq\r\n\r\nsq.gr.spatial_neighbors_radius(adata, spatial_key="spatial_um", radius=21,\r\n                               library_key="slide")\r\ngraph = adata.obsp["spatial_connectivities"].tocoo()\r\nslide = adata.obs["slide"].to_numpy()\r\nassert (slide[graph.row] == slide[graph.col]).all()\r\nsq.gr.nhood_enrichment(adata, cluster_key="cell_type", library_key="slide")\r\n<\/code><\/pre>\n
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