{"id":61501,"date":"2024-10-30T15:36:45","date_gmt":"2024-10-30T07:36:45","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61501"},"modified":"2024-10-30T15:36:45","modified_gmt":"2024-10-30T07:36:45","slug":"omada%e5%8c%85%ef%bc%9a%e6%97%a0%e7%9b%91%e7%9d%a3%e6%9c%ba%e5%99%a8%e5%ad%a6%e4%b9%a0%e5%8a%a9%e4%bd%a0%e7%a9%bf%e8%b6%8a%e5%9f%ba%e5%9b%a0%e8%a1%a8%e8%be%be%e8%b0%b1%e7%9a%84%e8%81%9a%e7%b1%bb","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61501","title":{"rendered":"Omada\u5305\uff1a\u65e0\u76d1\u7763\u673a\u5668\u5b66\u4e60\u52a9\u4f60\u7a7f\u8d8a\u57fa\u56e0\u8868\u8fbe\u8c31\u7684\u805a\u7c7b\u8ff7\u5bab\uff01"},"content":{"rendered":"\n<p><\/p>\n\n\n\n<p>\u563f\u670b\u53cb\u4eec\uff0c\u6b22\u8fce\u6765\u5230\u751f\u7269\u4fe1\u606f\u5b66\u7684\u7cbe\u5f69\u4e16\u754c\uff01\u4eca\u5929\uff0c\u5c0f\u679c\u5c06\u5e26\u9886\u5927\u5bb6\u4e00\u8d77\u5b66\u4e60R\u5305Omada\uff0c\u8fd9\u662f\u4e00\u6b3e\u65e0\u76d1\u7763\u673a\u5668\u5b66\u4e60\u5de5\u5177\uff0c\u5b83\u80fd\u591f\u81ea\u52a8\u5bf9\u57fa\u56e0\u8868\u8fbe\u8c31\u8fdb\u884c\u6837\u672c\u805a\u7c7b\uff0c\u4e3a\u6211\u4eec\u63ed\u793a\u590d\u6742\u75be\u75c5\u4e2d\u5206\u5b50\u72b6\u6001\u7684\u5dee\u5f02\u3002<\/p>\n\n\n\n<p>\u5728RNA\u5206\u6790\u7814\u7a76\u4e2d\uff0c\u63a2\u7d22\u6027\u805a\u7c7b\u5206\u6790\u9700\u8981\u5bf9\u4f17\u591a\u53c2\u6570\u8fdb\u884c\u9009\u62e9\uff0c\u8fd9\u8981\u6c42\u5bf9\u673a\u5668\u5b66\u4e60\u6709\u6df1\u5165\u4e86\u89e3\u5e76\u8fdb\u884c\u5927\u91cf\u7684\u8ba1\u7b97\u5b9e\u9a8c\u3002Omada\u901a\u8fc7\u81ea\u52a8\u5316\u7684\u673a\u5668\u5b66\u4e60\u529f\u80fd\uff0c\u4f7f\u5f97\u65e0\u76d1\u7763\u805a\u7c7b\u8f6c\u5f55\u7ec4\u6570\u636e\u66f4\u52a0\u65b9\u4fbf\u5feb\u6377\u3002\u5373\u4f7f\u5728\u751f\u7269\u5b66\u533a\u5206\u4e0d\u592a\u660e\u663e\u7684\u6570\u636e\u96c6\u4e2d\uff0c\u5b83\u4e5f\u80fd\u5e2e\u52a9\u6211\u4eec\u627e\u5230\u5177\u6709\u4e0d\u540c\u8868\u8fbe\u8c31\u548c\u4e34\u5e8a\u5173\u8054\u7684\u7a33\u5b9a\u4e9a\u7ec4\u3002<strong>\u6ce8\u610f\u54e6\uff0cGLAD<\/strong><strong>\u5305\u64cd\u4f5c\u5360\u7528\u5185\u5b58\u6bd4\u8f83\u5927\uff0c\u5efa\u8bae\u4f7f\u7528\u670d\u52a1\u5668<\/strong><strong>\u54e6<\/strong><strong>\uff0c\u6b22\u8fce\u8054\u7cfb\u5c0f\u679c\u79df\u8d41\u6027\u4ef7\u6bd4\u9ad8\u7684\u670d\u52a1\u5668<\/strong><strong>~<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u4e0b\u9762\uff0c\u5c0f\u679c\u5c06\u5f15\u9886\u5927\u5bb6\u9010\u6b65\u638c\u63e1\u64cd\u4f5c\u6d41\u7a0b\uff0c\u4ece\u5206\u6790\u6570\u636e\u96c6\u7684\u805a\u7c7b\u53ef\u884c\u6027\u5f00\u59cb\uff0c\u5230\u9009\u62e9\u6700\u4f18\u805a\u7c7b\u65b9\u6cd5\uff0c\u518d\u5230\u9009\u62e9\u6700\u4f18\u7279\u5f81\uff0c\u4f30\u8ba1\u6700\u4f18\u805a\u7c7b\u6570\u91cf\uff0c\u6700\u540e\u8fd0\u884c\u6700\u4f18\u805a\u7c7b\uff0c\u6211\u4eec\u5c06\u4e00\u540c\u7a7f\u8d8a\u57fa\u56e0\u8868\u8fbe\u8c31\u7684\u805a\u7c7b\u8ff7\u5bab\u3002<strong>\u5982\u679c\u4f60\u5728\u65c5\u9014\u4e2d\u9047\u5230\u4efb\u4f55\u56f0\u96be\uff0c\u522b\u62c5\u5fc3\uff0c\u5c0f\u679c\u968f\u65f6\u5f85\u547d\uff0c\u8bb0\u5f97\u8054\u7cfb\u5c0f\u679c\u4e3a\u4f60\u89e3\u7b54\u7591\u60d1~<\/strong><strong><\/strong><\/p>\n\n\n\n<p>\u6211\u4eec\u5148\u5b89\u88c5\u5e76\u52a0\u8f7domada\u5305\uff1a<\/p>\n\n\n\n<p>if (!require(&#8220;BiocManager&#8221;, quietly = TRUE))<\/p>\n\n\n\n<p>&nbsp;&nbsp;install.packages(&#8220;BiocManager&#8221;)<\/p>\n\n\n\n<p>BiocManager::install(&#8220;omada&#8221;)<\/p>\n\n\n\n<p>library(omada)<\/p>\n\n\n\n<ul>\n<li>\u6570\u636e\u96c6\u7684\u805a\u7c7b\u53ef\u884c\u6027<\/li>\n<\/ul>\n\n\n\n<p>\u7b2c\u4e00\u6b65\uff0c\u6211\u4eec\u9700\u8981\u6839\u636e\u6570\u636e\u96c6\u7684\u7ef4\u5ea6\uff08\u6837\u672c\u548c\u7279\u5f81\u5927\u5c0f\uff09\u8c03\u67e5\u5176\u805a\u7c7b\u7684\u53ef\u884c\u6027\u3002\u4e3a\u4e86\u7814\u7a76\u6570\u636e\u96c6\u7684\u805a\u7c7b\u53ef\u884c\u6027\uff0comada\u5305\u63d0\u4f9b\u4e86\u4e24\u4e2a\u7a33\u5b9a\u6027\u8bc4\u4f30\u6a21\u62df\u51fd\u6570\uff0c\u5b83\u4eec\u6a21\u62df\u7279\u5b9a\u7ef4\u5ea6\u7684\u6570\u636e\u96c6\u5e76\u8ba1\u7b97\u4e00\u7cfb\u5217\u805a\u7c7b\u7684\u6570\u636e\u96c6\u7a33\u5b9a\u6027\u3002<\/p>\n\n\n\n<p>&nbsp;\u7b2c\u4e00\u4e2a\u51fd\u6570\u662ffeasibilityAnalysis() \uff0c\u5b83\u4e3a\u7279\u5b9a\u6570\u91cf\u7684\u7c7b\u3001\u6837\u672c\u548c\u7279\u5f81\u751f\u6210\u4e00\u4e2a\u72ec\u7acb\u6570\u636e\u96c6\uff0c\u8be5\u6570\u636e\u96c6\u5305\u542b\u4e864\u4e2a\u7c7b\u522b(classes)\u300150\u4e2a\u6837\u672c(samples)\u548c15\u4e2a\u7279\u5f81(features)\u3002<\/p>\n\n\n\n<p># Selecting dimensions and number of clusters<\/p>\n\n\n\n<p>new.dataset.analysis &lt;- feasibilityAnalysis(classes = 4, samples = 50, features = 15)<\/p>\n\n\n\n<p>\u7b2c\u4e8c\u4e2a\u51fd\u6570\u662ffeasibilityAnalysisDataBased()\uff0c\u5b83\u63a5\u53d7\u73b0\u6709\u6570\u636e\u96c6\uff0c\u63d0\u53d6\u7279\u5b9a\u6570\u91cf\u805a\u7c7b\u7684\u7edf\u8ba1\u6570\u636e\uff08\u5e73\u5747\u503c\u548c\u6807\u51c6\u5dee\uff09\uff0c\u8be5\u6570\u636e\u96c6\u57fa\u4e8etoy_genes\u6570\u636e\u96c6\uff0c\u5305\u542b\u4e863\u4e2a\u7c7b\u522b\u3002<\/p>\n\n\n\n<p># Basing the simulation on an existing dataset and selecting the number of clusters<\/p>\n\n\n\n<p>existing.dataset.analysis &lt;- feasibilityAnalysisDataBased(data = toy_genes, classes = 3)<\/p>\n\n\n\n<p>\u63a5\u7740\uff0c\u8c03\u7528\u4ee5\u4e0b\u51fd\u6570\u6765\u63d0\u53d6\u8fd9\u4e24\u79cd\u5206\u6790\u65b9\u6cd5\u7684\u7ed3\u679c\uff1a<\/p>\n\n\n\n<ul>\n<li>get_average_stabilities_per_k\uff1a\u83b7\u53d6\u6bcf\u4e2a\u805a\u7c7b\u6570k\u7684\u5e73\u5747\u7a33\u5b9a\u6027<\/li>\n\n\n\n<li>get_max_stability\uff1a\u83b7\u53d6\u65b0\u6570\u636e\u96c6\u5206\u6790\u5bf9\u8c61\u7684\u6700\u5927\u7a33\u5b9a\u6027<\/li>\n\n\n\n<li>get_average_stability\uff1a\u83b7\u53d6\u65b0\u6570\u636e\u96c6\u5206\u6790\u5bf9\u8c61\u7684\u5e73\u5747\u7a33\u5b9a\u6027<\/li>\n\n\n\n<li>get_generated_dataset\uff1a\u83b7\u53d6\u65b0\u6570\u636e\u96c6\u5206\u6790\u5bf9\u8c61\u751f\u6210\u7684\u6570\u636e\u96c6<\/li>\n<\/ul>\n\n\n\n<p># Extract results of either function<\/p>\n\n\n\n<p>average.sts.k &lt;- get_average_stabilities_per_k(new.dataset.analysis) #<\/p>\n\n\n\n<p>maximum.st &lt;- get_max_stability(new.dataset.analysis)<\/p>\n\n\n\n<p>average.st &lt;- get_average_stability(new.dataset.analysis)<\/p>\n\n\n\n<p>generated.ds &lt;- get_generated_dataset(new.dataset.analysis)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"469\" height=\"50\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257911144_165816E8-7DFF-4e7d-A6E4-0F051F2A6F85.png?resize=469%2C50\" alt=\"\" class=\"wp-image-61502\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257911144_165816E8-7DFF-4e7d-A6E4-0F051F2A6F85.png?w=469 469w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257911144_165816E8-7DFF-4e7d-A6E4-0F051F2A6F85.png?resize=300%2C32 300w\" sizes=\"(max-width: 469px) 100vw, 469px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u8bf7\u6ce8\u610f\uff0c\u8fd9\u4e9b\u4f30\u8ba1\u503c\u4ec5\u4f5c\u4e3a\u6570\u636e\u96c6\u662f\u5426\u9002\u5408\u805a\u7c7b\u7684\u6307\u793a\uff0c\u800c\u4e0d\u662f\u8d28\u91cf\u7684\u5b9e\u9645\u8861\u91cf\u6807\u51c6\uff0c\u56e0\u4e3a\u5b83\u4eec\u4e0d\u8003\u8651\u6570\u636e\u4e2d\u7684\u5b9e\u9645\u4fe1\u53f7\uff0c\u800c\u53ea\u8003\u8651\u6837\u672c\u3001\u7279\u5f81\u548c\u805a\u7c7b\u6570\u91cf\u4e4b\u95f4\u7684\u5173\u7cfb\u3002<\/p>\n\n\n\n<p>\u4e8c\u3001\u81ea\u52a8\u805a\u7c7b\u5206\u6790<\/p>\n\n\n\n<p>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u4f7f\u7528 omada()\u6765\u8fd0\u884c\u6574\u4e2a\u5206\u6790\u5de5\u5177\u5305\uff0c\u81ea\u52a8\u5316\u805a\u7c7b\u51b3\u7b56\u5e76\u751f\u6210\u4f30\u8ba1\u7684\u6700\u4f73\u7c07\u3002 omada()\u7684\u8f93\u5165\u662f\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u6846\u548c\u8981\u8003\u8651\u7684\u7c07\u6570\u4e0a\u9650 k\u3002\u5c0f\u679c\u63d0\u9192\u5927\u5bb6\uff0c\u5728\u8fd0\u884c\u4efb\u4f55\u5de5\u5177\u4e4b\u524d\uff0c\u90fd\u4e0d\u8981\u5fd8\u4e86\u63d0\u524d\u5220\u9664\u6216\u4f30\u7b97 NA \u503c\u54e6\u3002<\/p>\n\n\n\n<p># Running the whole cascade of tools inputting an expression dataset<\/p>\n\n\n\n<p># and the upper k (number of clusters) to be investigated<\/p>\n\n\n\n<p>omada.analysis &lt;- omada(toy_genes, method.upper.k = 6)<\/p>\n\n\n\n<p>\u63a5\u7740\uff0c\u6211\u4eec\u53ef\u4ee5\u5229\u7528\u5404\u79cd\u51fd\u6570\u63d0\u53d6\u5f97\u5230\u4e0b\u5217\u8fd9\u4e9b\u5206\u6790\u7ed3\u679c\uff0c\u4f8b\u5982\u7279\u5f81\u9009\u62e9\u5206\u6570\uff08fs.scores\uff09\u3001\u6700\u4f73\u7279\u5f81\u9009\u62e9\u7ed3\u679c\uff08fs.optimal.features\uff09\u3001\u805a\u7c7b\u6295\u7968\u5206\u6570\uff08cv.scores\uff09\u3001\u6837\u672c\u7684\u6210\u5458\u5173\u7cfb\uff08sample.memberships\uff09\u7b49\u7b49\u3002<\/p>\n\n\n\n<p># Extract results<\/p>\n\n\n\n<p>pa.scores &lt;- get_partition_agreement_scores(omada.analysis)<\/p>\n\n\n\n<p>fs.scores &lt;- get_feature_selection_scores(omada.analysis)<\/p>\n\n\n\n<p>fs.optimal.features &lt;- get_feature_selection_optimal_features(omada.analysis)<\/p>\n\n\n\n<p>fs.optimal.number.of.features&lt;-get_feature_selection_optimal_number_of_features(omada.analysis)<\/p>\n\n\n\n<p>cv.scores &lt;- get_cluster_voting_scores(omada.analysis)<\/p>\n\n\n\n<p>cv.memberships &lt;- get_cluster_voting_memberships(omada.analysis)<\/p>\n\n\n\n<p>cv.metrics.votes &lt;- get_cluster_voting_metric_votes(omada.analysis)<\/p>\n\n\n\n<p>cv.k.votes &lt;- get_cluster_voting_k_votes(omada.analysis)<\/p>\n\n\n\n<p>sample.memberships &lt;- get_sample_memberships(omada.analysis)<\/p>\n\n\n\n<p>\u6700\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u7ed8\u5236\u4e0d\u540c\u7684\u7ed3\u679c\u56fe\uff0c\u5982\u5206\u533a\u534f\u8bae\u56fe\u3001\u7279\u5f81\u9009\u62e9\u56fe\u3001\u805a\u7c7b\u6295\u7968\u56fe\u7b49\uff0c\u5e2e\u52a9\u6211\u4eec\u66f4\u597d\u5730\u7406\u89e3\u6570\u636e\u96c6\u7684\u7ed3\u6784\u3001\u7279\u5f81\u9009\u62e9\u60c5\u51b5\u4ee5\u53ca\u805a\u7c7b\u7ed3\u679c\uff0c\u4e3a\u8fdb\u4e00\u6b65\u7684\u6570\u636e\u5206\u6790\u548c\u89e3\u91ca\u63d0\u4f9b\u91cd\u8981\u53c2\u8003\u3002<\/p>\n\n\n\n<p># Plot results<\/p>\n\n\n\n<p>plot_partition_agreement(omada.analysis)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"509\" height=\"321\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257924732_D564F9DD-CB7F-4fa6-9AF4-A8A7A4AC6FE4.png?resize=509%2C321\" alt=\"\" class=\"wp-image-61503\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257924732_D564F9DD-CB7F-4fa6-9AF4-A8A7A4AC6FE4.png?w=509 509w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257924732_D564F9DD-CB7F-4fa6-9AF4-A8A7A4AC6FE4.png?resize=300%2C189 300w\" sizes=\"(max-width: 509px) 100vw, 509px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5206\u533a\u4e00\u81f4\u6027\u56fe\u663e\u793a\u4e86\u5728\u4e0d\u540c\u805a\u7c7b\u6570\uff08k\u503c\uff09\u4e0b\uff0c\u6570\u636e\u96c6\u5185\u90e8\u7684\u5206\u533a\u4e00\u81f4\u6027\u548c\u7a33\u5b9a\u6027\u3002x\u8f74\u4ee3\u8868\u805a\u7c7b\u6570\uff08k\u503c\uff09\uff0cy\u8f74\u4ee3\u8868<a>\u5206\u533a<\/a>\u4e00\u81f4\u6027\u5f97\u5206\uff08Partition Agreement Score\uff09\u3002\u968f\u7740\u805a\u7c7b\u6570\u7684\u589e\u52a0\uff0c\u5206\u533a\u4e00\u81f4\u6027\u5206\u6570\u4f1a\u53d8\u5316\uff0c\u901a\u5e38\u5728\u4e00\u4e2a\u8f83\u9ad8\u7684\u5206\u533a\u4e00\u81f4\u6027\u5f97\u5206\u9644\u8fd1\u9009\u62e9\u6700\u4f73\u7684\u805a\u7c7b\u6570\uff08\u6700\u4f73k\u503c\uff09\u3002\u8fd9\u4e2a\u56fe\u53ef\u4ee5\u5e2e\u52a9\u786e\u5b9a\u6570\u636e\u96c6\u5728\u54ea\u4e2a\u805a\u7c7b\u6570\u4e0b\u8868\u73b0\u6700\u4f73\uff0c\u4ee5\u9009\u62e9\u5408\u9002\u7684\u805a\u7c7b\u6570\u7528\u4e8e\u8fdb\u4e00\u6b65\u5206\u6790\u548c\u89e3\u91ca\u3002<\/p>\n\n\n\n<p>plot_feature_selection(omada.analysis)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"492\" height=\"304\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257935316_FACE9C4B-2F57-4491-92B7-FFABE5210685.png?resize=492%2C304\" alt=\"\" class=\"wp-image-61504\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257935316_FACE9C4B-2F57-4491-92B7-FFABE5210685.png?w=492 492w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257935316_FACE9C4B-2F57-4491-92B7-FFABE5210685.png?resize=300%2C185 300w\" sizes=\"(max-width: 492px) 100vw, 492px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u7279\u5f81\u9009\u62e9\u56fe\u5c55\u793a\u4e86\u5728\u4e0d\u540c\u7279\u5f81\u9009\u62e9\u6570\u91cf\u4e0b\uff0c\u7279\u5f81\u9009\u62e9\u6548\u679c\u7684\u6bd4\u8f83\u3002\u8fd9\u4e2a\u56fe\u53ef\u4ee5\u5e2e\u52a9\u8bc6\u522b\u54ea\u79cd\u7279\u5f81\u9009\u62e9\u65b9\u6cd5\u5728\u6570\u636e\u96c6\u4e2d\u8868\u73b0\u6700\u4f73\uff0c\u6709\u52a9\u4e8e\u63d0\u9ad8\u540e\u7eed\u5206\u6790\u7684\u51c6\u786e\u6027\u548c\u6548\u679c\u3002<\/p>\n\n\n\n<p>plot_cluster_voting(omada.analysis)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"483\" height=\"301\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257948164_67F9C293-1B68-4f13-8380-761646462285.png?resize=483%2C301\" alt=\"\" class=\"wp-image-61505\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257948164_67F9C293-1B68-4f13-8380-761646462285.png?w=483 483w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257948164_67F9C293-1B68-4f13-8380-761646462285.png?resize=300%2C187 300w\" sizes=\"(max-width: 483px) 100vw, 483px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u805a\u7c7b\u6295\u7968\u56fe\u5c55\u793a\u4e86\u805a\u7c7b\u65b9\u6cd5\u7684\u5f97\u5206\u67f1\u72b6\u56fe\uff0c\u663e\u793a\u4e86\u4e0d\u540c\u805a\u7c7b\u65b9\u6cd5\u7684\u5f97\u5206\uff0c\u53ef\u53c2\u8003\u5404\u805a\u7c7b\u65b9\u6cd5\u5728\u6570\u636e\u96c6\u4e0a\u7684\u8868\u73b0\u3002<\/p>\n\n\n\n<p>\u4e09\u3001<a>\u9009\u62e9\u6700\u4f18\u805a\u7c7b\u65b9\u6cd5<\/a><\/p>\n\n\n\n<p>\u7b2c\u4e09\u6b65\uff0c\u6211\u4eec\u53ef\u4ee5\u6839\u636e\u6570\u636e\u96c6\u9009\u62e9\u6700\u5408\u9002\u7684\u805a\u7c7b\u65b9\u6cd5\u3002\u4f7f\u7528 clusteringMethodSelection() \u51fd\u6570\u6bd4\u8f83\u4e09\u79cd\u4e0d\u540c\u65b9\u6cd5\uff08\u5373\u8c31\u805a\u7c7b\u3001k \u5747\u503c\u805a\u7c7b\u3001\u5c42\u6b21\u805a\u7c7b\uff09\u7684\u5185\u90e8\u5206\u533a\u4e00\u81f4\u6027\u3002\u6211\u4eec\u53ef\u4ee5\u5b9a\u4e49\u4e0a\u9650 k \u4ee5\u53ca\u6bcf\u79cd\u65b9\u6cd5\u7684\u5185\u90e8\u6bd4\u8f83\u6b21\u6570\u3002\u6bd4\u8f83\u6b21\u6570\u7684\u589e\u52a0\u4f1a\u5e26\u6765\u66f4\u9ad8\u7684\u7a33\u5065\u6027\u548c\u6700\u9ad8\u7684\u8fd0\u884c\u65f6\u95f4\u3002<\/p>\n\n\n\n<p># Selecting the upper k limit and number of comparisons<\/p>\n\n\n\n<p>method.results &lt;- clusteringMethodSelection(toy_genes, method.upper.k = 3, number.of.comparisons = 2)<\/p>\n\n\n\n<p># Extract results<\/p>\n\n\n\n<p>pa.scores &lt;- get_partition_agreement_scores(method.results)<\/p>\n\n\n\n<p># Plot results<\/p>\n\n\n\n<p>plot_partition_agreement(method.results)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"410\" height=\"256\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257961171_E18171E8-841C-4d0e-93B2-7BC3D9D68CF6.png?resize=410%2C256\" alt=\"\" class=\"wp-image-61506\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257961171_E18171E8-841C-4d0e-93B2-7BC3D9D68CF6.png?w=410 410w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257961171_E18171E8-841C-4d0e-93B2-7BC3D9D68CF6.png?resize=300%2C187 300w\" sizes=\"(max-width: 410px) 100vw, 410px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u5206\u6790\u4e0a\u56fe\uff0c\u6211\u4eec\u53ef\u4ee5\u53d1\u73b0\uff0c\u4f7f\u7528\u8c31\u805a\u7c7b\uff08\u7eff\u8272\u7ebf\uff09\u7684\u5206\u533a\u4e00\u81f4\u6027\u5f97\u5206\u6700\u9ad8\uff08k_maen=0.53\uff09\uff0c\u56e0\u6b64\u5728\u540e\u7eed\u7684\u6b65\u9aa4\u4e2d\uff0c\u6211\u4eec\u53ef\u4ee5\u6307\u5b9a\u4f7f\u7528\u8c31\u805a\u7c7b\u7684\u65b9\u6cd5\u3002<\/p>\n\n\n\n<p>Omada\u5305\u8fd8\u63d0\u4f9b\u4e86\u901a\u8fc7\u5229\u7528\u51fd\u6570partitionAgreement()\u5355\u72ec\u8ba1\u7b97\u4e24\u4e2a\u7279\u5b9a\u805a\u7c7b\u65b9\u6cd5\u548c\u53c2\u6570\u96c6\u4e4b\u95f4\u7684\u5206\u533a\u4e00\u81f4\u6027\u7684\u51fd\u6570\uff0c\u8be5\u51fd\u6570\u9700\u8981\u9009\u62e9\u4e24\u79cd\u7b97\u6cd5\u3001\u5ea6\u91cf\u548c\u805a\u7c7b\u6570\u91cf\u3002<\/p>\n\n\n\n<p># Selecting algorithms, measures and number of clusters<\/p>\n\n\n\n<p>agreement.results &lt;- partitionAgreement(toy_genes, algorithm.1 = &#8220;spectral&#8221;, measure.1 = &#8220;rbfdot&#8221;, algorithm.2 = &#8220;kmeans&#8221;,measure.2 = &#8220;Lloyd&#8221;, number.of.clusters = 3)<\/p>\n\n\n\n<p># Extract results<\/p>\n\n\n\n<p>pa.scores &lt;- get_agreement_scores(agreement.results)<\/p>\n\n\n\n<p>\u56db\u3001\u9009\u62e9\u6700\u4f18\u7279\u5f81<\/p>\n\n\n\n<p>\u4e3a\u4e86\u9009\u62e9\u63d0\u4f9b\u6700\u7a33\u5b9a\u805a\u7c7b\u7684\u7279\u5f81\uff0c\u51fd\u6570 featureSelection() \u9700\u8981\u6700\u5c0f\u548c\u6700\u5927\u805a\u7c7b\u6570 (k) \u4ee5\u53ca\u51b3\u5b9a\u6bcf\u4e2a\u7279\u5f81\u96c6\u589e\u52a0\u7387\u7684\u7279\u5f81\u6b65\u9aa4\u3002\u5728\u672c\u4f8b\u4e2d\uff0c\u6211\u4eec\u9009\u62e9\u4e86\u6700\u5c0f\u805a\u7c7b\u6570\u4e3a3\uff0c\u6700\u5927\u805a\u7c7b\u6570\u4e3a6\uff0c\u5e76\u8bbe\u7f6e\u4e86\u6bcf\u4e2a\u7279\u5f81\u96c6\u589e\u52a0\u7387\u7684\u7279\u5f81\u6b65\u9aa4\u4e3a3\u3002<\/p>\n\n\n\n<p># Selecting minimum and maximum number of clusters and feature step<\/p>\n\n\n\n<p>feature.selection.results &lt;- &nbsp;featureSelection(toy_genes, min.k = 3, max.k = 6,&nbsp;step = 3)<\/p>\n\n\n\n<p>\u4ece\u7ed3\u679c\u4e2d\u63d0\u53d6\u5e73\u5747\u7279\u5f81\u7a33\u5b9a\u6027\u5f97\u5206\uff0c\u6700\u4f73\u7279\u5f81\u6570\u4ee5\u53ca\u6700\u4f73\u7279\u5f81\u96c6\u3002\u5e73\u5747\u7279\u5f81\u7a33\u5b9a\u6027\u5f97\u5206\u53ef\u4ee5\u5e2e\u52a9\u8bc4\u4f30\u4e0d\u540c\u7279\u5f81\u96c6\u7684\u7a33\u5b9a\u6027\uff0c\u6700\u4f73\u7279\u5f81\u6570\u5219\u6307\u793a\u4e86\u5728\u7ed9\u5b9a\u805a\u7c7b\u8303\u56f4\u5185\u6240\u9009\u62e9\u7684\u6700\u4f73\u7279\u5f81\u6570\u91cf\u3002<\/p>\n\n\n\n<p># Extract results<\/p>\n\n\n\n<p>feature.selection.scores &lt;- get_average_feature_k_stabilities(feature.selection.results)<\/p>\n\n\n\n<p>optimal.number.of.features &lt;- get_optimal_number_of_features<\/p>\n\n\n\n<p>optimal.features &lt;- get_optimal_features(feature.selection.results)<\/p>\n\n\n\n<p>\u901a\u8fc7\u7ed8\u5236\u5e73\u5747\u7a33\u5b9a\u6027\u7ed3\u679c\u56fe\uff0c\u53ef\u4ee5\u76f4\u89c2\u5730\u89c2\u5bdf\u4e0d\u540c\u7279\u5f81\u6570\u91cf\u4e0b\u7684\u7a33\u5b9a\u6027\u5f97\u5206\u8d8b\u52bf\uff0c\u4ece\u800c\u66f4\u597d\u5730\u7406\u89e3\u54ea\u4e9b\u7279\u5f81\u6570\u91cf\u7ec4\u5408\u63d0\u4f9b\u4e86\u6700\u7a33\u5b9a\u7684\u805a\u7c7b\u7ed3\u679c\u3002<\/p>\n\n\n\n<p># Plot results<\/p>\n\n\n\n<p>plot_average_stabilities(feature.selection.results)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"290\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257978772_C10A9F74-9FA2-4a1c-9AAB-0E146D442876.png?resize=554%2C290\" alt=\"\" class=\"wp-image-61507\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257978772_C10A9F74-9FA2-4a1c-9AAB-0E146D442876.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730257978772_C10A9F74-9FA2-4a1c-9AAB-0E146D442876.png?resize=300%2C157 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u4e94\u3001\u4f30\u8ba1\u6700\u4f18\u805a\u7c7b\u6570\u91cf<\/p>\n\n\n\n<p>\u901a\u8fc7\u4f7f\u7528clusterVoting()\u51fd\u6570\uff0c\u6211\u4eec\u53ef\u4ee5\u6839\u636e\u5185\u90e8\u6307\u6807\u96c6\u5408\u4f30\u8ba1\u6700\u5408\u9002\u7684\u805a\u7c7b\u6570\uff0c\u5e76\u9009\u62e9\u8981\u8003\u8651\u7684\u6700\u5c0f\u548c\u6700\u5927\u805a\u7c7b\u6570\u4ee5\u53ca\u6240\u9009\u7b97\u6cd5\uff08\u201csc\u201d \u8868\u793a\u8c31\u805a\u7c7b\uff0c\u201ckm\u201d \u8868\u793ak \u5747\u503c\u805a\u7c7b\uff0c\u201chr\u201d \u8868\u793a\u5c42\u6b21\u805a\u7c7b\uff09\u8fdb\u884c\u805a\u7c7b\u6295\u7968\u3002\u5728\u672c\u4f8b\u4e2d\uff0c\u6211\u4eec\u9009\u62e9\u5c06\u6700\u5c0f\u805a\u7c7b\u6570\u8bbe\u4e3a4\uff0c\u6700\u5927\u805a\u7c7b\u6570\u8bbe\u4e3a8\uff0c\u5e76\u9009\u62e9\u8c31\u805a\u7c7b\u7b97\u6cd5\u8fdb\u884c\u805a\u7c7b\u6295\u7968\u3002<\/p>\n\n\n\n<p><a><\/a># Selecting minimum and maximum number of clusters and algorithm to be used<\/p>\n\n\n\n<p>cluster.voting.results &lt;- clusterVoting(toy_genes, 4,8,&#8221;sc&#8221;)<\/p>\n\n\n\n<p>\u4ece\u7ed3\u679c\u4e2d\u63d0\u53d6\u5185\u90e8\u6307\u6807\u5f97\u5206\u3001\u805a\u7c7b\u6210\u5458\u5173\u7cfb\u4ee5\u53ca\u6295\u7968\u9891\u7387\u7b49\u76f8\u5173\u6307\u6807\u6570\u636e\uff0c\u5e76\u5229\u7528\u8fd9\u4e9b\u6570\u636e\u6765\u8bc4\u4f30\u4e0d\u540c\u805a\u7c7b\u6570\u4e0b\u7684\u5185\u90e8\u6307\u6807\u8868\u73b0\u53ca\u6700\u5408\u9002\u7684\u805a\u7c7b\u6570\u3002<\/p>\n\n\n\n<p># Extract results<\/p>\n\n\n\n<p>internal.metric.scores &lt;- get_internal_metric_scores(cluster.voting.results)<\/p>\n\n\n\n<p>cluster.memberships.k &lt;- get_cluster_memberships_k(cluster.voting.results)<\/p>\n\n\n\n<p>metric.votes.k &lt;- get_metric_votes_k(cluster.voting.results)<\/p>\n\n\n\n<p>vote.frequencies.k &lt;- get_vote_frequencies_k(cluster.voting.results)<\/p>\n\n\n\n<p>\u901a\u8fc7\u7ed8\u5236\u6295\u7968\u9891\u7387\u7ed3\u679c\u56fe\uff0c\u53ef\u4ee5\u76f4\u89c2\u5730\u5c55\u793a\u5728\u8003\u8651\u4e0d\u540c\u805a\u7c7b\u6570\u548c\u6240\u9009\u7b97\u6cd5\u7684\u60c5\u51b5\u4e0b\u5404\u4e2a\u5185\u90e8\u6307\u6807\u5f97\u51fa\u7684\u6295\u7968\u9891\u7387\uff0c\u5e2e\u52a9\u6211\u4eec\u7406\u89e3\u54ea\u4e2a\u805a\u7c7b\u6570\u6700\u53d7\u5185\u90e8\u6307\u6807\u7684\u652f\u6301\u3002<\/p>\n\n\n\n<p># Plot results<\/p>\n\n\n\n<p>plot_vote_frequencies(cluster.voting.results)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"554\" height=\"325\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730258001763_74953C5B-B5C4-4978-9128-772740829C40.png?resize=554%2C325\" alt=\"\" class=\"wp-image-61508\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730258001763_74953C5B-B5C4-4978-9128-772740829C40.png?w=554 554w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730258001763_74953C5B-B5C4-4978-9128-772740829C40.png?resize=300%2C176 300w\" sizes=\"(max-width: 554px) 100vw, 554px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<ul>\n<li>\u8fd0\u884c\u6700\u4f18\u805a\u7c7b<\/li>\n<\/ul>\n\n\n\n<p>\u6700\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u57fa\u4e8e\u4e0a\u9762\u83b7\u5f97\u7684\u6700\u4f18\u7684\u53c2\u6570\uff0c\u4f7f\u7528optimalClustering() \u6765\u8fd0\u884c\u6700\u4f18\u805a\u7c7b\u5566\uff01\u8fd9\u4e2a\u51fd\u6570\u8fd8\u4f1a\u81ea\u52a8\u8fd0\u884c\u53ef\u80fd\u7684\u7b97\u6cd5\u53c2\u6570\uff0c\u4fdd\u7559\u7a33\u5b9a\u6027\u6700\u9ad8\u7684\u7b97\u6cd5\u53c2\u6570\u3002<\/p>\n\n\n\n<p># Running the clustering with specific number of clusters(k) and algorithm<\/p>\n\n\n\n<p>sample.memberships &lt;- optimalClustering(toy_genes, 4, &#8220;spectral&#8221;)<\/p>\n\n\n\n<p># Extract results<\/p>\n\n\n\n<p>memberships &lt;- get_optimal_memberships(sample.memberships)<\/p>\n\n\n\n<p>optimal.stability &lt;- get_optimal_stability_score(sample.memberships)<\/p>\n\n\n\n<p>optimal.parameter &lt;- get_optimal_parameter_used(sample.memberships)<\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img decoding=\"async\" loading=\"lazy\" width=\"312\" height=\"32\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730258089352_F51466F0-C2E2-4878-B267-11F2DDF1CA23.png?resize=312%2C32\" alt=\"\" class=\"wp-image-61509\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730258089352_F51466F0-C2E2-4878-B267-11F2DDF1CA23.png?w=312 312w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/10\/1730258089352_F51466F0-C2E2-4878-B267-11F2DDF1CA23.png?resize=300%2C32 300w\" sizes=\"(max-width: 312px) 100vw, 312px\" data-recalc-dims=\"1\" \/><\/figure>\n\n\n\n<p>\u6700\u7ec8\uff0c\u6211\u4eec\u53ef\u4ee5\u63d0\u53d6\u6700\u4f18\u7684\u7ed3\u679c\uff1a\u6700\u4f18\u7684\u805a\u7c7b\u7ed3\u679c\u5b58\u50a8\u5728memberships\u4e2d\uff0c\u53ef\u4ee5\u5bf9\u805a\u7c7b\u7ed3\u679c\u8fdb\u884c\u8fdb\u4e00\u6b65\u5206\u6790\u548c\u53ef\u89c6\u5316\u3002\u6700\u4f18\u7684\u7a33\u5b9a\u6027\u5206\u6570\u4e3a0.715\uff0c\u8868\u660e\u805a\u7c7b\u7ed3\u679c\u7684\u7a33\u5b9a\u6027\u8f83\u9ad8\u3002\u4f7f\u7528\u4e86\u6700\u4f18\u7684\u7b97\u6cd5\u53c2\u6570rbfdot\uff0c\u8fd9\u8868\u660e\u5728\u8fd9\u4e2a\u53c2\u6570\u8bbe\u7f6e\u4e0b\u5f97\u5230\u4e86\u6700\u4f18\u7684\u805a\u7c7b\u7ed3\u679c\u3002<\/p>\n\n\n\n<p>\u7efc\u5408\u4ee5\u4e0a\u7ed3\u679c\uff0c\u6211\u4eec\u5f97\u5230\u4e86\u7a33\u5b9a\u4e14\u9ad8\u6548\u7684\u6700\u4f18\u805a\u7c7b\u7ed3\u679c\uff0c\u53ef\u7528\u4e8e\u540e\u7eed\u7684\u6570\u636e\u5206\u6790\u548c\u6316\u6398\u3002<\/p>\n\n\n\n<p>\u600e\u4e48\u6837\uff0cAI\u7684\u4e16\u754c\u662f\u4e0d\u662f\u5f88\u795e\u5947\uff1f\u597d\u5566\uff0c\u5c0f\u679c\u5df2\u7ecf\u5e26\u9886\u5927\u5bb6\u4e00\u8d77\u5b8c\u6210\u4e86<a><\/a>Omada\u5305\u7684\u521d\u6b65\u63a2\u7d22\uff0c\u4f60\u6709\u6ca1\u6709\u5bf9AI\u5728\u57fa\u56e0\u8868\u8fbe\u8c31\u7684\u805a\u7c7b\u4e0a\u7684\u5e94\u7528\u6709\u4e86\u611f\u6027\u7684\u8ba4\u8bc6\u5462\uff1f\u73b0\u5728\uff0c\u4f60\u53ef\u4ee5\u5f00\u59cb\u5c55\u5f00\u81ea\u5df1\u7684\u5b9e\u8df5\uff0c\u5229\u7528omada\u5305\u6765\u6784\u5efa\u5c5e\u4e8e\u4f60\u81ea\u5df1\u7684\u6a21\u578b\u5566\uff01<\/p>\n\n\n\n<p>\u65e0\u8bba\u4f60\u662f\u5728\u4f18\u5316\u4ee3\u7801\uff0c\u8fd8\u662f\u5728\u4e91\u7aef\u8fdb\u884c\u4fbf\u6377\u7684\u5206\u6790\uff0c\u4e91\u751f\u4fe1\u795e\u5668\u90fd\u80fd\u4e3a\u4f60\u63d0\u4f9b\u5f3a\u5927\u7684\u652f\u6301\u3002<strong>\u6b22\u8fce<\/strong><strong>\u8bd5\u8bd5\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u795e\u5668<\/strong><strong>\uff0c<\/strong><strong>\u53ea\u9700<\/strong><strong>\u4e00\u952e<\/strong><strong>\u4e0a\u4f20\u6570\u636e\uff0c\u60f3\u8981\u7684\u56fe\u5c31\u80fd\u8f7b\u677e<\/strong><strong>get~<\/strong><strong><\/strong><\/p>\n\n\n\n<p><strong>\u4e91\u751f\u4fe1\u5e73\u53f0\u94fe\u63a5\uff1a<\/strong><a href=\"http:\/\/www.biocloudservice.com\/home.html\"><strong>http:\/\/www.biocloudservice.com\/home.html<\/strong><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u563f\u670b\u53cb\u4eec\uff0c\u6b22\u8fce\u6765\u5230\u751f\u7269\u4fe1\u606f\u5b66\u7684\u7cbe\u5f69\u4e16\u754c\uff01\u4eca\u5929\uff0c\u5c0f\u679c\u5c06\u5e26\u9886\u5927\u5bb6\u4e00\u8d77\u5b66\u4e60R\u5305Omada\uff0c\u8fd9\u662f\u4e00\u6b3e\u65e0\u76d1\u7763\u673a\u5668\u5b66\u4e60\u5de5\u5177 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61501"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=61501"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61501\/revisions"}],"predecessor-version":[{"id":61510,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61501\/revisions\/61510"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61501"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61501"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61501"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}