{"id":68938,"date":"2026-11-14T21:06:58","date_gmt":"2026-11-14T13:06:58","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=68938"},"modified":"2026-11-14T21:06:58","modified_gmt":"2026-11-14T13:06:58","slug":"giotto-suite-z-plane-transcript-polygon-overlap","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/giotto-suite-z-plane-transcript-polygon-overlap\/","title":{"rendered":"Giotto Suite \u91cc\u4e00\u4e2a\u5206\u5b50\u7b97\u5728\u54ea\u4e2a\u7ec6\u80de\uff1f\u5148\u628a\u7126\u9762\u548c\u8fb9\u754c\u5bf9\u4e0a"},"content":{"rendered":"
\n

\u540c\u4e00\u5757\u7ec4\u7ec7\uff0c\u6309\u7ec6\u80de\u7edf\u8ba1\u65f6\u67d0\u4e2a\u6807\u8bb0\u6709\u51e0\u5341\u4e2a\u5206\u5b50\uff0c\u6539\u6309\u7ec6\u80de\u6838\u7edf\u8ba1\u5c31\u53ea\u5269\u51e0\u4e2a\u3002\u8fd8\u6709\u4e00\u79cd\u66f4\u9690\u853d\u7684\u60c5\u51b5\uff0c\u660e\u660e\u4ee5\u4e3a\u53ea\u5206\u6790\u4e00\u4e2a\u7126\u9762\uff0c\u7b97\u51fa\u7684\u7ed3\u679c\u5374\u628a\u4e0d\u540c\u6df1\u5ea6\u7684\u5206\u5b50\u6295\u5728\u540c\u4e00\u5f20\u5e73\u9762\u4e0a\u3002Giotto Suite \u53ef\u4ee5\u540c\u65f6\u4fdd\u5b58\u56fe\u50cf\u3001\u5206\u5b50\u70b9\u5750\u6807\u548c\u591a\u4e2a\u7a7a\u95f4\u5355\u4f4d\u7684\u591a\u8fb9\u5f62\uff0c\u8fd9\u7ed9\u4e86\u7814\u7a76\u8005\u5f88\u5927\u7684\u9009\u62e9\u4f59\u5730\u3002\u7b2c\u4e00\u6b65\u662f\u660e\u786e\u7edf\u8ba1\u4e2d\u7684\u4e00\u4e2a\u89c2\u6d4b\u7a76\u7adf\u4ee3\u8868\u6574\u7ec6\u80de\u3001\u4e00\u4e2a\u6838\u3001\u4e00\u4e2a\u7126\u9762\u8f6e\u5ed3\uff0c\u8fd8\u662f\u4e00\u4e2a\u56fa\u5b9a\u5927\u5c0f\u7684\u7f51\u683c\u3002<\/p>\n

\u4ece\u4e00\u4e2a\u771f\u5b9e\u7684\u5206\u5b50\u70b9\u5411\u5916\u8ffd\u67e5<\/h2>\n

\u6311\u4e00\u4e2a\u76ee\u6807\u57fa\u56e0\u7684\u5206\u5b50\uff0c\u5148\u8bb0\u5f55\u5176\u7269\u7406\u5750\u6807\u3001\u7126\u9762\u6216\u6df1\u5ea6\u3001\u5b9e\u9a8c\u89c6\u91ce\u548c\u552f\u4e00\u6807\u8bc6\u3002\u518d\u53d6\u540c\u4e00\u89c6\u91ce\u7684\u7ec6\u80de\u4e0e\u6838\u591a\u8fb9\u5f62\uff0c\u68c0\u67e5\u4e8c\u8005\u91c7\u7528\u7684\u5355\u4f4d\u548c\u539f\u70b9\u3002\u5916\u90e8\u56fe\u50cf\u5206\u6790\u8f6f\u4ef6\u6709\u65f6\u8f93\u51fa\u50cf\u7d20\u4f4d\u7f6e\uff0c\u5206\u5b50\u8868\u53ef\u80fd\u7528\u5fae\u7c73\u3002\u82e5\u4e00\u4fa7\u7528\u6574\u5f20\u62fc\u63a5\u56fe\u539f\u70b9\u3001\u53e6\u4e00\u4fa7\u7528\u88c1\u526a\u533a\u57df\u5de6\u4e0a\u89d2\uff0c\u5c31\u7b97\u4e24\u4e2a\u6570\u90fd\u53eb\u6a2a\u7eb5\u5750\u6807\uff0c\u4e5f\u4e0d\u5728\u540c\u4e00\u4e2a\u53c2\u8003\u6846\u67b6\u91cc\u3002\u5148\u627e\u4e09\u4e2a\u4e0d\u5171\u7ebf\u5730\u6807\u4f5c\u914d\u51c6\uff0c\u518d\u8c08\u5206\u5b50\u5f52\u5c5e\u3002<\/p>\n

Giotto \u7684\u7a7a\u95f4\u5355\u4f4d\u53ef\u4ee5\u5e76\u5b58\u3002\u4e00\u4e2a\u7ec6\u80de\u6709\u81ea\u5df1\u7684\u8fb9\u754c\u548c\u7f16\u53f7\uff0c\u4e0e\u5176\u5173\u8054\u7684\u6838\u6709\u53e6\u4e00\u5957\u8fb9\u754c\u548c\u7f16\u53f7\u3002\u540c\u4e00\u4e2a\u5206\u5b50\u82e5\u65e2\u4f4d\u4e8e\u6838\u91cc\u4e5f\u4f4d\u4e8e\u6574\u7ec6\u80de\u91cc\uff0c\u5728\u6838\u77e9\u9635\u548c\u7ec6\u80de\u77e9\u9635\u4e2d\u5404\u8ba1\u4e00\u6b21\u672c\u6765\u5408\u7406\uff0c\u56e0\u4e3a\u5b83\u4eec\u662f\u5bf9\u540c\u4e00\u5bf9\u8c61\u7684\u4e24\u79cd\u6d4b\u91cf\u8303\u56f4\u3002\u82e5\u8bef\u628a\u4e24\u5f20\u77e9\u9635\u6309\u7ec6\u80de\u540d\u5bf9\u9f50\u540e\u76f4\u63a5\u76f8\u52a0\uff0c\u6838\u5185\u5206\u5b50\u5c31\u4f1a\u88ab\u91cd\u590d\u8ba1\u7b97\u3002\u8981\u8ba1\u7b97\u80de\u8d28\u5206\u5b50\uff0c\u9700\u5728\u540c\u4e00\u7ec6\u80de\u3001\u76f8\u540c\u7126\u9762\u548c\u660e\u786e\u7684\u5305\u542b\u5173\u7cfb\u4e0b\u6c42\u5dee\uff0c\u6216\u8005\u76f4\u63a5\u5728\u5bf9\u5e94\u51e0\u4f55\u533a\u57df\u91cd\u65b0\u7edf\u8ba1\u3002Giotto \u7a7a\u95f4\u805a\u5408\u7684\u5b98\u65b9\u793a\u4f8b<\/a><\/p>\n

\u56db\u4e2a\u5206\u5b50\u6f14\u793a\u7126\u9762\u548c\u51e0\u4f55\u8303\u56f4\u600e\u6837\u6539\u53d8\u7ed3\u679c<\/h2>\n

\u8bbe\u6709\u4e00\u4efd\u7b80\u5316\u7684\u4e09\u7ef4\u6210\u50cf\u6570\u636e\u3002\u96f6\u53f7\u7126\u9762\u4e0a\u4e00\u679a\u7ec6\u80de\u7684\u8303\u56f4\u7528\u6a2a\u7eb5\u5750\u6807\u5747\u5728\u96f6\u5230\u5341\u4e4b\u95f4\u7684\u65b9\u5f62\u4ee3\u66ff\uff0c\u6838\u7684\u8303\u56f4\u662f\u6a2a\u7eb5\u5750\u6807\u5747\u5728\u56db\u5230\u516d\u4e4b\u95f4\u3002\u8fd9\u4e2a\u7ec6\u80de\u5f62\u72b6\u662f\u6559\u5b66\u8fd1\u4f3c\u3002\u8868\u91cc\u56db\u679a\u90fd\u662f\u540c\u4e00\u57fa\u56e0\u7684\u5206\u5b50\uff0c\u6211\u4eec\u8981\u95ee\u7684\u662f\uff0c\u54ea\u4e9b\u80fd\u8ba1\u5165\u201c\u96f6\u53f7\u7126\u9762\u4e0a\u7684\u8fd9\u679a\u7ec6\u80de\u201d\u4ee5\u53ca\u5176\u4e2d\u7684\u6838\u3002<\/p>\n

\n\n\n\n\n\n\n\n\n
\u5206\u5b50<\/th>\n\u6a2a\u3001\u7eb5\u5750\u6807<\/th>\n\u7126\u9762<\/th>\n\u5bf9\u96f6\u53f7\u7126\u9762\u8fd9\u679a\u7ec6\u80de\u7684\u5224\u65ad<\/th>\n<\/tr>\n<\/thead>\n
\u7532<\/td>\n5\u30015<\/td>\n\u96f6<\/td>\n\u65e2\u5728\u7ec6\u80de\u4e5f\u5728\u6838\u5185<\/td>\n<\/tr>\n
\u4e59<\/td>\n8\u30015<\/td>\n\u96f6<\/td>\n\u5728\u7ec6\u80de\u5185\uff0c\u5728\u6838\u5916<\/td>\n<\/tr>\n
\u4e19<\/td>\n5\u30015<\/td>\n\u4e00<\/td>\n\u5e73\u9762\u4f4d\u7f6e\u91cd\u5408\uff0c\u4f46\u6765\u81ea\u53e6\u4e00\u7126\u9762<\/td>\n<\/tr>\n
\u4e01<\/td>\n12\u30015<\/td>\n\u96f6<\/td>\n\u843d\u5728\u8be5\u7ec6\u80de\u8f6e\u5ed3\u4ee5\u5916<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\"\u5e73\u9762\u5750\u6807\u76f8\u540c\uff0c\u4e5f\u7b97\u540c\u4e00\u679a\u5417\u3002\u6559\u5b66\u7b97\u4f8b\uff5c\u7ec6\u80de\u3001\u6838\u3001\u7126\u9762\u662f\u4e09\u4e2a\u9700\u8981\u5206\u522b\u6838\u5bf9\u7684\u6761\u4ef6\u3002\u7532\u3001\u4e59\uff0c\u90fd\u5728\u96f6\u53f7\u9762\u7684\u7ec6\u80de\u8f6e\u5ed3\uff0c\u53ea\u6709\u7532\u4e5f\u843d\u5728\u6838\u8fb9\u754c\u5185\u3002\u4e19\uff0c\u6a2a\u7eb5\u5750\u6807\u548c\u7532\u76f8\u540c\uff0c\u7126\u9762\u4e0d\u540c\uff0c\u4e0d\u80fd\u76f4\u63a5\u8ba1\u5165\u96f6\u53f7\u9762\u7684\u7ec6\u80de\u3002\u4e01\uff0c\u5728\u8f6e\u5ed3\u5916\uff0c\u4fdd\u7559\u672a\u5206\u914d\u72b6\u6001\uff0c\u518d\u68c0\u67e5\u51e0\u4f55\u914d\u51c6\u3002\"
\u6559\u5b66\u7b97\u4f8b\uff5c\u7ec6\u80de\u3001\u6838\u3001\u7126\u9762\u662f\u4e09\u4e2a\u9700\u8981\u5206\u522b\u6838\u5bf9\u7684\u6761\u4ef6\u3002<\/figcaption><\/figure>\n

\u7b5b\u5b9a\u96f6\u53f7\u9762\u540e\uff0c\u8fd9\u679a\u7ec6\u80de\u8ba1\u4e24\u4e2a\uff0c\u6838\u8ba1\u4e00\u4e2a\u3002\u5982\u679c\u628a\u4e0d\u540c\u7126\u9762\u7684\u6240\u6709\u5206\u5b50\u5148\u6295\u5230\u5e73\u9762\uff0c\u518d\u5957\u7528\u96f6\u53f7\u9762\u7684\u8f6e\u5ed3\uff0c\u5c31\u4f1a\u628a\u4e19\u4e5f\u7eb3\u5165\uff0c\u6574\u7ec6\u80de\u8ba1\u4e09\u4e2a\uff0c\u6838\u8ba1\u4e24\u4e2a\u3002\u8fd9\u4e2a\u5dee\u503c\u76f4\u63a5\u6765\u81ea\u7b5b\u9009\u6761\u4ef6\uff0c\u4e0d\u80fd\u7528\u6765\u8bf4\u660e\u57fa\u56e0\u53d1\u751f\u6838\u5185\u5bcc\u96c6\u3002\u53cd\u8fc7\u6765\uff0c\u82e5\u672c\u6765\u7684\u76ee\u6807\u5c31\u662f\u505a\u5168\u539a\u5ea6\u6295\u5f71\uff0c\u4e5f\u53ef\u4ee5\u505a\uff0c\u4f46\u5e94\u4f7f\u7528\u4e0e\u6295\u5f71\u76ee\u7684\u76f8\u5339\u914d\u7684\u5206\u5272\u3001\u53bb\u91cd\u548c\u7f16\u53f7\u65b9\u6848\uff0c\u6e05\u695a\u544a\u8bc9\u8bfb\u8005\u5b9e\u9645\u5728\u6570\u4ec0\u4e48\u3002\u4ec5\u51ed\u5e73\u9762\u6a2a\u7eb5\u5750\u6807\u6070\u597d\u91cd\u5408\u4e5f\u4e0d\u5e94\u628a\u7532\u4e0e\u4e19\u5f53\u4f5c\u540c\u4e00\u6b21\u68c0\u6d4b\uff0c\u56e0\u4e3a\u5206\u5b50\u6807\u8bc6\u548c\u7126\u9762\u4e0d\u540c\u3002<\/p>\n

\u7528\u5339\u914d\u7684\u7126\u9762\u8ba1\u7b97\u70b9\u4e0e\u591a\u8fb9\u5f62\u7684\u91cd\u53e0<\/h2>\n

\u5b98\u65b9\u793a\u4f8b\u53ef\u4ee5\u663e\u5f0f\u9009\u53d6\u4e00\u7ec4\u591a\u8fb9\u5f62\uff0c\u540c\u65f6\u9650\u5236\u7279\u5f81\u70b9\u7684\u6df1\u5ea6\u5b57\u6bb5\uff0c\u7136\u540e\u5c06\u91cd\u53e0\u7ed3\u679c\u8f6c\u6210\u8ba1\u6570\u77e9\u9635\u3002\u4e0b\u4f8b\u5047\u5b9a\u5bf9\u8c61\u7684\u8fb9\u754c\u96c6\u540d\u79f0\u5c31\u662f\u96f6\u53f7\u7126\u9762\uff0c\u7279\u5f81\u70b9\u4e2d\u6709\u76f8\u5e94\u7684\u6df1\u5ea6\u5217\uff0c\u5f53\u524d\u7279\u5f81\u7c7b\u578b\u4e3a\u5f85\u7edf\u8ba1\u7684\u5206\u5b50\u3002\u5b9e\u9645\u9879\u76ee\u8981\u5148\u67e5\u5bf9\u8c61\u4e2d\u5b58\u7684\u540d\u79f0\u548c\u53d6\u503c\uff0c\u4e0d\u80fd\u56e0\u4e3a\u793a\u4f8b\u53eb\u96f6\u53f7\u5c31\u5957\u5728\u6240\u6709\u4eea\u5668\u8f93\u51fa\u4e0a\u3002\u6df1\u5ea6\u53ef\u80fd\u662f\u7126\u9762\u7f16\u53f7\uff0c\u4e5f\u53ef\u80fd\u662f\u8fde\u7eed\u7684\u7269\u7406\u5750\u6807\uff0c\u9700\u8981\u636e\u6b64\u9009\u62e9\u5339\u914d\u65b9\u5f0f\u3002\u91cd\u53e0\u8ba1\u7b97\u53c2\u6570<\/a> \u00b7 \u91cd\u53e0\u7ed3\u679c\u5982\u4f55\u8f6c\u6210\u77e9\u9635<\/a><\/p>\n

library(Giotto)\r\ng0 <- calculateOverlap(g, spatial_info = "z0",\r\n                       feat_subset_column = "global_z",\r\n                       feat_subset_ids = 0)\r\ng0 <- overlapToMatrix(g0)\r\n<\/code><\/pre>\n
\u5bf9\u6574\u4e2a\u5207\u7247\u6c47\u603b\u524d\uff0c\u53ef\u4ee5\u62bd\u5341\u4e2a\u7ed3\u6784\u8f83\u6e05\u695a\u7684\u7ec6\u80de\uff0c\u624b\u5de5\u7ed8\u5236\u51e0\u4e2a\u4ee3\u8868\u57fa\u56e0\u7684\u5206\u5b50\u548c\u8f6e\u5ed3\u3002\u81f3\u5c11\u80fd\u56de\u7b54\u8fd9\u4e9b\u95ee\u9898\uff0c\u70b9\u662f\u5426\u96c6\u4e2d\u5728\u9884\u671f\u533a\u57df\uff0c\u5916\u90e8\u70b9\u662f\u5426\u88ab\u8bef\u8ba1\uff0c\u6709\u6ca1\u6709\u76f8\u90bb\u8fb9\u754c\u4ea4\u53e0\uff0c\u4ee5\u53ca\u540c\u4e00\u6761\u5206\u5b50\u6807\u8bc6\u662f\u5426\u88ab\u591a\u4e2a\u540c\u7ea7\u5bf9\u8c61\u91cd\u590d\u9886\u53d6\u3002\u82e5\u591a\u8fb9\u5f62\u76f8\u4e92\u4ea4\u53e0\uff0c\u4e0d\u80fd\u9ed8\u8ba4\u4efb\u4e00\u9879\u76ee\u90fd\u4f1a\u66ff\u4f60\u7528\u540c\u4e00\u79cd\u89c4\u5219\u9009\u62e9\u6240\u5c5e\u7ec6\u80de\u3002\u5e94\u67e5\u770b\u91cd\u53e0\u5173\u7cfb\u548c\u6700\u7ec8\u77e9\u9635\uff0c\u660e\u786e\u4fdd\u7559\u51b2\u7a81\u3001\u6392\u9664\u51b2\u7a81\u8fd8\u662f\u6309\u6709\u4f9d\u636e\u7684\u65b9\u5f0f\u88c1\u51b3\uff0c\u5e76\u62a5\u544a\u53d7\u5f71\u54cd\u7684\u5206\u5b50\u6570\u3002<\/p>\n
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\u6211\u4eec\u5728 R 4.3.3 \u4e2d\u5b89\u88c5\u4e86 Giotto Suite \u7684\u5bf9\u8c61\u4e0e\u91cd\u53e0\u8ba1\u7b97\u7ec4\u4ef6 GiottoClass 0.3.5\uff0c\u914d\u5408 terra 1.7.65 \u5c06\u8868\u4e2d\u7684\u56db\u679a\u5206\u5b50\u5efa\u6210\u70b9\uff0c\u5206\u522b\u4e0e\u65b9\u5f62\u7ec6\u80de\u548c\u6838\u7684\u591a\u8fb9\u5f62\u76f8\u4ea4\u3002\u91c7\u7528\u8be5\u7248\u672c\u9762\u5411\u7a7a\u95f4\u5411\u91cf\u7684\u91cd\u53e0\u51fd\u6570\uff0c\u6307\u5b9a\u6df1\u5ea6\u5217\u4e3a\u7126\u9762\u7f16\u53f7\u5e76\u7b5b\u9009\u96f6\u53f7\u540e\uff0c\u7ec6\u80de\u5185\u8fd4\u56de\u6709\u6548\u7f16\u53f7\u7684\u662f\u7532\u548c\u4e59\uff0c\u6838\u5185\u53ea\u6709\u7532\u3002\u4fdd\u7559\u6240\u6709\u7126\u9762\u65f6\uff0c\u4e19\u540c\u65f6\u8fdb\u5165\u4e86\u8fd9\u679a\u7ec6\u80de\u548c\u6838\u7684\u4e8c\u7ef4\u8303\u56f4\uff0c\u4e01\u59cb\u7ec8\u5728\u754c\u5916\u3002\u8fd9\u6837\u53ea\u6539\u6df1\u5ea6\u7b5b\u9009\u5c31\u80fd\u91cd\u73b0\u524d\u9762\u7684\u624b\u7b97\u3002\u672c\u6b21\u6240\u7528 GiottoClass \u7248\u672c\u7684\u91cd\u53e0\u8ba1\u7b97\u5b9e\u73b0<\/a><\/p>\n
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