{"id":54146,"date":"2024-06-16T13:42:41","date_gmt":"2024-06-16T05:42:41","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=54146"},"modified":"2026-09-11T23:07:49","modified_gmt":"2026-09-11T15:07:49","slug":"%e3%80%90%e6%89%8b%e6%8a%8a%e6%89%8b%e6%95%99%e4%bd%a0%e3%80%91cytoscape-%e5%9f%ba%e5%9b%a0%e4%ba%92%e4%bd%9c%e7%bd%91%e7%bb%9c%e5%9b%be%e7%9a%84%e4%bf%9d%e5%a7%86%e7%ba%a7%e8%ae%b2%e8%a7%a3","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/%e3%80%90%e6%89%8b%e6%8a%8a%e6%89%8b%e6%95%99%e4%bd%a0%e3%80%91cytoscape-%e5%9f%ba%e5%9b%a0%e4%ba%92%e4%bd%9c%e7%bd%91%e7%bb%9c%e5%9b%be%e7%9a%84%e4%bf%9d%e5%a7%86%e7%ba%a7%e8%ae%b2%e8%a7%a3\/","title":{"rendered":"\u3010\u624b\u628a\u624b\u6559\u4f60\u3011Cytoscape\u2014\u57fa\u56e0\u4e92\u4f5c\u7f51\u7edc\u56fe\u7684\u4fdd\u59c6\u7ea7\u8bb2\u89e3"},"content":{"rendered":"<aside class=\"ysx-source-note\"><span>\u6765\u6e90<\/span><\/p>\n<p>\u516c\u4f17\u53f7\u300c\u751f\u4fe1\u56fe\u300d\u5386\u53f2\u5185\u5bb9\uff1b\u672c\u6587\u4fdd\u7559\u539f\u6709\u6280\u672f\u4fe1\u606f\u5e76\u4f18\u5316\u7f51\u9875\u6392\u7248\u3002 <a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=MzkxODUxNDgzNA==&amp;mid=2247484145&amp;idx=1&amp;sn=2380abbac6976bf5b716aac1ba53b9b6\" target=\"_blank\" rel=\"noopener noreferrer nofollow\">\u67e5\u770b\u539f\u6587<\/a><\/p>\n<\/aside>\n<p>\u5927\u5bb6\u8fd8\u8bb0\u4e0d\u8bb0\u5f97\u5c0f\u56fe\u4e4b\u524d\u6709\u63d0\u8fc7Cytoscape\uff0c\u4eca\u5929\u5c31\u662f\u5c0f\u56fe\u7ed9\u5927\u5bb6\u5151\u73b0\u627f\u8bfa\u7684\u65f6\u5019\uff01<\/p>\n<h2>Cytoscape \u9002\u5408\u505a\u4ec0\u4e48<\/h2>\n<p>Cytoscape\u662f\u4e00\u6b3e\u4f7f\u7528\u5f88\u5e7f\u6cdb\u7684\u7f51\u7edc\u56fe\u7ed8\u5236\u7f8e\u5316\u8f6f\u4ef6\uff0c\u662f\u73b0\u5728\u7ec4\u5b66\u6570\u636e\u540e\u671f\u5904\u7406\u4e0d\u53ef\u6216\u7f3a\u7684\u597d\u7528\u5de5\u5177\uff0c\u4eca\u5929\u5c0f\u56fe\u5c31\u7ed9\u5927\u5bb6\u8be6\u7ec6\u4ecb\u7ecd\u4e0bCytoscape\u7684\u56fe\u7247\u7f8e\u5316\u64cd\u4f5c\u3002<\/p>\n<p>\u6211\u4eec\u9a6c\u4e0a\u5f00\u59cb\u5b66\u8d77\u6765~<\/p>\n<h2>\u51c6\u5907\u5e76\u5bfc\u5165\u7f51\u7edc\u6570\u636e<\/h2>\n<p><strong>\u9996\u5148\uff0c\u4f60\u5f97\u5148\u4e0b\u8f7dCytoscape<\/strong><\/p>\n<p>\uff081\uff09\u5bfc\u5165STRING\u4e92\u4f5c\u5206\u6790\u7ed3\u679c\u6570\u636e\u201cstring_interactions_short.tsv\u201d\uff0c\u6570\u636e\u4e2dnode1\u4e0enode2\u4e3a\u4e00\u5bf9\u8282\u70b9\uff0ccombined_score\u4e3a\u4e92\u4f5c\u5206\u6570\u3002<\/p>\n<p>\u5bfc\u5165\u9014\u5f84\uff1aFile-&gt;Import-&gt;Network from File-&gt;OK\u3002\u64cd\u4f5c\u754c\u9762\u5982\u4e0b\u56fe\uff1a<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_1ymy7FWiaRdv0oVHzyrDk4ibItvsXw.jpg?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p>\uff082\uff09\u8fdb\u884c\u8282\u70b9\u9009\u62e9\u3002\u64cd\u4f5c\u754c\u9762\u5982\u4e0b\u56fe\uff1a<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_KFs0AIFLGFNrXr5GfPJt46d0Oib2Hw.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p>\uff083\uff09\u5bf9\u5bfc\u5165\u7684\u6570\u636e\u8fdb\u884c\u7f51\u7edc\u5316\u5206\u6790\uff1a\u5728\u5de5\u5177\u680f\u4e2d\u9009\u62e9Tools-&gt;Analysis Network-&gt;OK\u3002\u64cd\u4f5c\u754c\u9762\u5982\u4e0b\u56fe\uff1a<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_4NVIXHYmIv6MCQaGFHSmfvfIsVMPsA.jpg?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p>\uff084\uff09\u5982\u679c\u6ca1\u6709\u5c0f\u4f19\u4f34\u60f3\u8981\u7684\u7c7b\u578b\u53ef\u4ee5\u8fdb\u884c\u81ea\u5df1\u6784\u5efa\uff0c\u6bd4\u5982\u57fa\u56e0\u6570\u76ee\u8f83\u591a\uff0c\u53ef\u4ee5\u91c7\u7528\u540c\u5fc3\u5706\u7684\u5c55\u793a\u7c7b\u578b\u3002\u5728\u5de5\u5177\u680f\u4e2d\u9009\u62e9Style-&gt;\u4e09-&gt;Create New Style\u3002\u64cd\u4f5c\u754c\u9762\u5982\u4e0b\u56fe\uff1a<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_hk4VhhUPksriaUZibINCIQEgxtsLeQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_cvAtClOpfqx0sgHz1Z6LKf1ICvCl6Q.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p>\u662f\u4e0d\u662f\u53d1\u73b0\u6ca1\u6709\u57fa\u56e0\u540d<\/p>\n<p>\uff085\uff09\u5728\u5de5\u5177\u680f\u4e2d\u9009\u62e9Style-&gt;label-shared name-&gt;Passthrough Mapping\u3002\u64cd\u4f5c\u754c\u9762\u5982\u4e0b\u56fe\uff1a<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_d57DlYaermpWlvKwdypVXenzEzDYOw.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p>\u8fd9\u6837\u540d\u5b57\u5c31\u663e\u73b0\u51fa\u6765\u4e86<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_30jTaA58O1Qunll8iaFkxOzOsxq40g.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p><strong>\u63a5\u4e0b\u6765\u5c31\u8981\u8fdb\u884c\u5c55\u793a\u7f51\u7edc\u7684\u7f8e\u5316<\/strong><\/p>\n<h2>\u7f8e\u5316\u8282\u70b9\u3001\u8fde\u7ebf\u4e0e\u7f51\u7edc\u5e03\u5c40<\/h2>\n<p>\u5bf9\u4e8e\u6700\u521d\u7248\u7684\u7f51\u7edc\u56fe\uff0c\u5c0f\u56fe\u76f8\u4fe1\u6ca1\u6709\u4eba\u4f1a\u89c9\u5f97\u597d\u770b\uff0c\u4e5f\u7edd\u5bf9\u6ee1\u8db3\u4e0d\u4e86\u6742\u5fd7\u7684\u8981\u6c42\uff0c\u90a3\u4e48\uff0c\u6211\u4eec\u5c31\u52a8\u624b\u7f8e\u5316\u5b83\u5427\u3002<\/p>\n<p>\u5176\u5b9eCytoscape\u7684\u53ef\u89c6\u5316\u754c\u9762\u975e\u5e38\u4eba\u6027\u5316\uff0c\u6309\u7167\u5c0f\u56fe\u4e0b\u9762\u7684\u6279\u6ce8\uff0c\u5927\u5bb6\u90fd\u70b9\u4e00\u70b9\uff0c\u5e94\u8be5\u5f88\u5feb\u5c31\u80fd\u638c\u63e1\u3002<\/p>\n<p>\u5728\u9875\u9762\u5de6\u4fa7\u9009\u62e9style(\u53c2\u6570\u9009\u62e9\u7248\u5757)\u5bf9\u7f51\u7edc\u56fe\u8fdb\u884c\u7f8e\u5316\u3002Cytoscape\u4e5f\u81ea\u5e26\u4e86\u7f8e\u5316\u6a21\u677f\uff0c\u5927\u5bb6\u53ef\u4ee5\u4f9d\u6b21\u5c1d\u8bd5\u6548\u679c\uff0c\u4e5f\u53ef\u4ee5\u6839\u636e\u7ed8\u56fe\u9700\u6c42\u5728\u57fa\u7840\u6a21\u677f\u4e0a\u8fdb\u884c\u53c2\u6570\u8c03\u6574\u3002<\/p>\n<p>style\u677f\u5757\u5206\u4e3a\u4e09\u4e2a\u7f8e\u5316\u6a21\u5757Node\u3001Edge\u548cNetwork\u3002Node\u662f\u7f8e\u5316\u8282\u70b9\uff0cEdge\u662f\u7f8e\u5316\u4e92\u4f5c\u5173\u7cfb\u7ebf\u3001Network\u662f\u4f5c\u7528\u4e8e\u6574\u5f20\u56fe\u3002<\/p>\n<p>\uff081\uff09\u66f4\u6539\u8282\u70b9\u5f62\u72b6\u548c\u5927\u5c0f\u3002<\/p>\n<p>\u9009\u62e9Shape-&gt;Ellipse-&gt;Apply\u5c06\u8282\u70b9\u5f62\u72b6\u6539\u4e3a\u5706\u5f62\u3002\u64cd\u4f5c\u754c\u9762\u5982\u4e0b\u56fe\uff1a<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_cJvB4XXmgK7iae6f8zEulPkDUVNebg.jpg?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p>\u9009\u62e9Height\u5c06\u8282\u70b9\u9ad8\u5ea6\u6539\u4e3a75;<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_NicicEuoiaK8nMlJCRH3A8rxcicnEQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p>\u9700\u8981\u6ce8\u610f\u7684\u662f\uff0c\u5728\u6bcf\u4e2a\u6a21\u5757\u4e0a\u90fd\u6709\u4e09\u5217\uff0cDef.\u5217\u4ee3\u8868\u53c2\u6570\u4e3a\u5168\u5c40\u53c2\u6570\uff0cMap.\u5217\u4ee3\u8868\u53c2\u6570\u968f\u4e92\u4f5c\u5173\u7cfb\u800c\u53d8\u5316\uff0cByn.\u5217\u4ee3\u8868\u53c2\u6570\u53ea\u4f5c\u7528\u4e8e\u6240\u9009\u67d0\u4e00\u8282\u70b9\u6216\u4e92\u4f5c\u5173\u7cfb\u3002<\/p>\n<p>\u5c06\u8282\u70b9\u7684\u5927\u5c0f\u6539\u4e3a\u8fde\u7eed\u53d8\u91cf\uff0c\u5f53\u4e00\u4e2a\u8282\u70b9\u4e0e\u5176\u5b83\u8282\u70b9\u7684\u4e92\u4f5c\u5173\u7cfb\u7ebf\u8d8a\u591a\u65f6\uff0c\u8282\u70b9\u8d8a\u5927\u3002\u9009\u62e9Map.\u5217\u7684Height-&gt;Column-&gt;Degree\uff0cMapping Type\u53c2\u6570\u9009\u62e9Continuous Mapping\u8fde\u7eed\u6620\u5c04\u3002\u64cd\u4f5c\u754c\u9762\u5982\u4e0b\u56fe\uff1a<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_hAEDTBKn4ZwlTWQb5La2gqyWgsV9ew.jpg?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p>\u5728\u8fde\u7eed\u6620\u5c04\u4e2d\uff0c\u8282\u70b9\u7684\u9ad8\u5ea6\u662f\u4e00\u4e2a\u8fde\u7eed\u53d8\u91cf\uff0c\u4e3a\u4e86\u9644\u548c\u4e0a\u56fe\u8282\u70b9\u9ad8\u5ea6\uff0c\u5c06\u53d8\u91cf\u6700\u5927\u503c\u6539\u4e3a75\uff0c\u6700\u5c0f\u503c\u6539\u4e3a30\u3002<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/11_FibWcRfuMLG77k5F2pV0uxYvrb3EAQ.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p>\u8282\u70b9\u7684\u5bbd\u5ea6Width\u5982\u4e0a\u64cd\u4f5c\u3002<\/p>\n<p>\uff082\uff09\u66f4\u6539\u4e92\u4f5c\u5173\u7cfb\u7ebf\u7684\u7c97\u7ec6<\/p>\n<p>\u5728Edge\u6a21\u5757\u4e2d\uff0c\u9009\u62e9Map.\u5217\u7684Width-&gt;Column-&gt;combined_score\uff0ccombined_score\u4ee3\u8868\u8282\u70b9\u4e4b\u95f4\u7684\u4e92\u4f5c\u5f3a\u5ea6\u3002Mapping Type\u53c2\u6570\u9009\u62e9Continuous Mapping\u8fde\u7eed\u6620\u5c04\u3002\u5728\u8fde\u7eed\u6620\u5c04\u4e2d\uff0c\u7ebf\u7684\u9ad8\u5ea6\u662f\u4e00\u4e2a\u8fde\u7eed\u53d8\u91cf\uff0c\u5c06\u53d8\u91cf\u6700\u5927\u503c\u6539\u4e3a5\uff0c\u6700\u5c0f\u503c\u6539\u4e3a1\u3002\u64cd\u4f5c\u754c\u9762\u5982\u4e0b\u56fe\uff1a<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/12_2wB81oibcAo3ULy0gJxBftky5ut5Nw.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<p>\uff083\uff09\u6570\u636e\u6316\u6398<\/p>\n<p>Cytoscape\u7684\u6570\u636e\u6316\u6398\u4e3b\u8981\u662f\u7528\u5230\u201c\u7b5b\u9009\u201d\u5de5\u5177\u3002\u7f51\u7edc\u56fe\u5e38\u89c1\u7684\u7b5b\u9009\u65b9\u5f0f\u662f\u5229\u7528\u8fde\u901a\u6027\u7b5b\u9009\u5173\u952e\u57fa\u56e0\uff0cCytoscape\u53ef\u4ee5\u76f4\u63a5\u8ba1\u7b97\u70b9\u7684\u8fde\u901a\u6027\uff08K\uff09\uff0c\u70b9\u51fb\u83dc\u5355\u680fTools-&gt;NetworkAnalyzer-&gt;Network analysis-&gt;Analyze Network\uff0c\u70b9\u51fb\u786e\u8ba4\uff0c\u8fde\u901a\u6027\u6570\u636e\u5c31\u4f1a\u51fa\u73b0\u5728\u201c\u70b9\u4fe1\u606f\u9875\u201d\uff0c\u5217\u540d\u4e3a\u201cdegree\u201d\u3002\u64cd\u4f5c\u754c\u9762\u5982\u4e0b\u56fe\uff1a<\/p>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/13_XgTibCCocUD7ugXyrMic0clwxYZroA.png?ssl=1\" loading=\"lazy\" decoding=\"async\" alt=\"\"><\/figure>\n<figure><img data-recalc-dims=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/14_wCjA4yRf4FKDBOQjRjy6FU1MeNlM6Q.png?ssl=1\" loading=\"lazy\" decoding=\"async\" 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