{"id":16071,"date":"2023-10-20T15:56:13","date_gmt":"2023-10-20T07:56:13","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=16071"},"modified":"2023-10-20T15:56:14","modified_gmt":"2023-10-20T07:56:14","slug":"nmf%e7%94%9f%e6%b6%a9%e9%9a%be%e6%87%82%ef%bc%9f%e5%b0%8f%e8%8a%b1%e5%b8%a6%e4%bd%a0%e8%b5%b0%e8%bf%9b%e9%99%8d%e7%bb%b4%e8%81%9a%e7%b1%bb%e7%9a%84%e4%b8%96%e7%95%8c%ef%bc%81","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=16071","title":{"rendered":"NMF\u751f\u6da9\u96be\u61c2\uff1f\u5c0f\u82b1\u5e26\u4f60\u8d70\u8fdb\u964d\u7ef4\u805a\u7c7b\u7684\u4e16\u754c\uff01"},"content":{"rendered":"<p>\u54c8\u55bd\u54c8\u55bd\uff0c\u4f60\u7684\u5c0f\u53ef\u7231\u5c0f\u82b1\u7a81\u7136\u51fa\u73b0~\u4eca\u5929\u548c\u5927\u5bb6\u804a\u4e00\u804aNMF\uff0c\u201c\u975e\u8d1f\u77e9\u9635\u5206\u89e3\u201d\uff0cNMF\u65b9\u6cd5\u5728\u751f\u4fe1\u9886\u57df\u975e\u5e38\u5173\u952e\uff0c\u53ef\u4ee5\u7528\u4e8e\u964d\u7ef4\u3001\u5f02\u5e38\u503c\u68c0\u6d4b\u3001\u7279\u5f81\u63d0\u53d6\u7b49\u7b49\u5f88\u591a\u65b9\u9762\uff0c\u5728\u8fdb\u884c\u5b9e\u64cd\u4e4b\u524d\uff0c\u5c0f\u82b1\u5148\u7ed9\u5927\u5bb6\u8bb2\u8bb2NMF\u975e\u8d1f\u77e9\u9635\u5206\u89e3\u7684\u539f\u7406\uff01<\/p>\n<p>\u9996\u5148\u60f3\u8c61\u4e00\u4e0b\u4f60\u6b63\u5728\u73a9\u62fc\u56fe\u6e38\u620f\u3002\u4f60\u6709\u4e00\u4e2a\u5de8\u5927\u7684\u3001\u5145\u6ee1\u5404\u79cd\u5f62\u72b6\u548c\u989c\u8272\u7684\u62fc\u56fe\uff0c\u8fd9\u5c31\u662f\u4f60\u7684\u975e\u8d1f\u77e9\u9635V\u3002\u73b0\u5728\uff0c\u4f60\u60f3\u8981\u5c06\u8fd9\u4e2a\u5de8\u5927\u7684\u62fc\u56fe\u5206\u6210\u4e24\u90e8\u5206\uff0c\u6bcf\u4e00\u90e8\u5206\u90fd\u662f\u7531\u4e00\u4e9b\u5c0f\u62fc\u56fe\u5757\u7ec4\u6210\u7684\uff0c\u8fd9\u4e9b\u5c0f\u62fc\u56fe\u5757\u53ef\u4ee5\u7ec4\u5408\u5728\u4e00\u8d77\u8fd8\u539f\u6210\u539f\u59cb\u62fc\u56fe\u3002<\/p>\n<p>\u6211\u4eec\u628a\u8fd9\u4e24\u90e8\u5206\u653e\u5230\u4e24\u4e2a\u7279\u6b8a\u7684\u76d2\u5b50\u91cc\uff0c\u4e00\u4e2a\u53ebW\u76d2\u5b50\uff0c\u800c\u53e6\u4e00\u4e2a\u53ebH\u76d2\u5b50\u3002\u8fd9\u4e24\u4e2a\u76d2\u5b50\u7684\u7279\u6b8a\u4e4b\u5904\u5728\u4e8e\uff0c\u91cc\u9762\u7684\u62fc\u56fe\u5757\u90fd\u662f\u975e\u8d1f\u7684\uff0c\u6ca1\u6709\u8d1f\u53f7\u6216\u9ed1\u6697\u7684\u62fc\u56fe\u5757\uff0c\u8bf4\u5230\u8fd9\u91cc\uff0c\u5c31\u548cNM\u8fd9\u90e8\u5206\u5355\u8bcd\u5bf9\u5e94\u4e0a\u5566\uff0c\u800c\u751f\u7269\u6570\u636e\u5f88\u591a\u90fd\u662f\u975e\u8d1f\u7684\uff0c\u5982\u679c\u5206\u89e3\u51fa\u8d1f\u503c\u5c31\u7f3a\u4e4f\u4e86\u751f\u7269\u5b66\u610f\u4e49\uff0c\u8fd9\u5c31\u4f7f\u5f97NMF\u76f8\u6bd4\u5947\u5f02\u503c\u5206\u89e3\uff08SVD\uff09\u7b49\u65b9\u6cd5\u6765\u8bf4\u66f4\u6709\u4f18\u52bf\u3002<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"248\" class=\"wp-image-16072\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-1.png?resize=640%2C248\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-1.png?w=854 854w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-1.png?resize=300%2C116 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-1.png?resize=768%2C298 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-1.png?resize=600%2C233 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u5728\u6211\u4eec\u62fc\u56fe\u7684\u8fc7\u7a0b\u4e2d\uff0c\u4f60\u53ef\u4ee5\u7528W\u548cH\u6765\u4ee3\u66ff\u539f\u59cb\u7684\u62fc\u56fe\uff0c\u5b9e\u73b0\u4e86\u6570\u636e\u7684\u964d\u7ef4\uff0c\u540c\u65f6\u51cf\u5c11\u4e86\u5b58\u50a8\u7a7a\u95f4\u7684\u9700\u6c42\u3002\u8fd9\u5c31\u597d\u50cf\u662f\u5c06\u4e00\u4e2a\u5e9e\u5927\u7684\u62fc\u56fe\uff0c\u53d8\u6210\u4e86\u4e00\u4e2a\u5c0f\u800c\u7cbe\u81f4\u7684\u62fc\u56fe\uff0c\u66f4\u5bb9\u6613\u7ba1\u7406\u548c\u5c55\u793a\u3002<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"555\" height=\"303\" class=\"wp-image-16073\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-2.png?resize=555%2C303\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-2.png?w=555 555w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-2.png?resize=300%2C164 300w\" sizes=\"(max-width: 555px) 100vw, 555px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u4e0a\u9762\u8fd9\u5f20\u56fe\u66f4\u5bb9\u6613\u7406\u89e3\uff0c\u5047\u8bbe\u539f\u5148\u662fM\u00d7N\u7684\u57fa\u56e0\u6837\u672c\u77e9\u9635\uff0c\u884c\u4e3a\u57fa\u56e0\uff0c\u5217\u4e3a\u6837\u672c\uff0c\u4e4b\u540e\u5c06\u5176\u5206\u4e3a\u4e86W\u77e9\u9635\u548cH\u77e9\u9635\uff0c\u5982\u679c\u7528H\u6765\u8868\u793a\u6574\u4e2a\u77e9\u9635\u964d\u7ef4\u540e\u7684\u7ed3\u679c\uff0c\u4fbf\u662f\u6bcf\u4e2a\u7ec6\u80de\u7528\u4e00\u4e2a\u4e8c\u7ef4\u5411\u91cf\u6765\u8868\u793a\uff0c\u8fd9\u6837\u5c31\u5b9e\u73b0\u4e86\u964d\u7ef4\uff0c\u4ece\u539f\u5148\u76847\u7ef4\u964d\u5230\u4e862\u7ef4\uff0c\u6bd4\u5982\u4e4b\u524d\u5728Seurat\u5305\u4e2d\u8fdb\u884cPCA\u964d\u7ef4\uff0c\u5c31\u53ef\u4ee5\u5c06RunPCA\u4e2d\u7684\u53c2\u6570pca\u6539\u4e3anmf\uff0c\u5177\u4f53\u53ef\u4ee5\u53c2\u8003\u4e0b\u9762\u8fd9\u6bb5\u4ee3\u7801\uff0c\u5c06\u539f\u59cb\u6570\u636e\u8fdb\u884c\u77e9\u9635\u5206\u89e3\u540e\u5c31\u53ef\u4ee5\u805a\u7c7b\uff0c\u5982\u679c\u8fd8\u662f\u6709\u5c0f\u4f19\u4f34\u4e0d\u61c2\uff0c\u53ef\u4ee5\u770b\u770b\u5c0f\u82b1\u4e4b\u524d\u8bb2\u7684Seurat\u5305\uff0c\u628a\u8fd9\u6bb5\u4ee3\u7801\u63d2\u8fdb\u53bb\u5c31\u597d\u5566\u3002<\/p>\n<p>vm &lt;- pbmc@assays$RNA@scale.data<\/p>\n<p>res &lt;- nmf(vm, 10, method = &#8220;snmf&#8221;, seed = &#8216;nndsvd&#8217;)<\/p>\n<p>## \u5206\u89e3\u7ed3\u679c\u8fd4\u56desuerat\u5bf9\u8c61<\/p>\n<p>pbmc@reductions$nmf &lt;- pbmc@reductions$pca<\/p>\n<p>pbmc@reductions$nmf@cell.embeddings &lt;- t(coef(res))<\/p>\n<p>pbmc@reductions$nmf@feature.loadings &lt;- basis(res)<\/p>\n<p>## \u4f7f\u7528nmf\u7684\u5206\u89e3\u7ed3\u679c\u964d\u7ef4\u805a\u7c7b<\/p>\n<p>set.seed(219)<\/p>\n<p>pbmc.nmf &lt;- RunUMAP(pbmc, reduction = &#8216;nmf&#8217;, dims = 1:10) %&gt;%<\/p>\n<p>NMF\u9664\u53bb\u964d\u7ef4\u5916\uff0c\u4e5f\u53ef\u4ee5\u7528\u4e8e\u805a\u7c7b\uff0c\u4e0d\u8fc7\u8fd9\u91cc\u7684\u805a\u7c7b\u6307\u7684\u662f\u4f7f\u7528\u964d\u7ef4\u540e\u5f97\u5230\u7684\u7279\u5f81\u7efc\u5408\u5df2\u77e5\u805a\u7c7b\u65b9\u6cd5\uff08\u5982K-meas\uff09\u8fdb\u884c\u805a\u7c7b\uff0c\u4e0b\u9762\u7ed9\u5927\u5bb6\u6f14\u793a\u4e00\u4e0b\u5982\u4f55\u7528R\u5305nmf\u5bf9\u4e00\u4e2a\u8868\u8fbe\u77e9\u9635\u8fdb\u884c\u805a\u7c7b\uff0c\u6216\u8005\u8bf4\u5bf9\u80bf\u7624\u8fdb\u884c\u5206\u578b\uff1a<\/p>\n<p>NMF\u8fd9\u4e2aR\u5305\u7684\u5b89\u88c5\u5f88\u7b80\u5355\uff0c\u53ea\u9700\u8981install.packages(\u2018NMF\u2019)\u5c31\u53ef\u4ee5\u5566\uff0c\u7ed9\u5927\u5bb6\u8bb2\u8bb2\u8fd9\u4e2a\u51fd\u6570\u7684\u53c2\u6570<\/p>\n<p><strong>nmf(x, rank,<\/strong><\/p>\n<p><strong> method, seed = nmf.getOption(&#8220;default.seed&#8221;),<\/strong><\/p>\n<p><strong> rng = NULL, nrun = if (length(rank) &gt; 1) 30 else 1,<\/strong><\/p>\n<p><strong> model = NULL, .options = list(),<\/strong><\/p>\n<p><strong> .pbackend = nmf.getOption(&#8220;pbackend&#8221;),<\/strong><\/p>\n<p><strong> .callback = NULL, &#8230;)<\/strong><\/p>\n<ul>\n<li><strong>x\uff1a\u8fd9\u91cc\u5c31\u662f\u6211\u4eec\u7684\u8868\u8fbe\u77e9\u9635\uff1b<\/strong><\/li>\n<li><strong>rank\uff1a\u7b80\u5355\u7406\u89e3\u662f\u5c31\u662f\u6211\u4eec\u60f3\u5206\u6210\u51e0\u4e2acluster\uff0c\u53ef\u4ee5\u662f\u4e00\u4e2a\u56fa\u5b9a\u7684\u6570\u503c\uff0c\u4e5f\u53ef\u4ee5\u662f\u4e00\u4e2a\u8303\u56f4\uff08\u4f8b\u59822\uff1a7\uff09<\/strong><\/li>\n<li><strong>method:\u5c31\u662fNMF\u7b97\u6cd5\u7684\u9009\u62e9\uff0c\u603b\u5171\u670911\u79cd\uff0c\u53ef\u901a\u8fc7nmfAlgorithm()\u51fd\u6570\u67e5\u770b\uff0c\u9ed8\u8ba4brunet<\/strong><\/li>\n<\/ul>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"90\" class=\"wp-image-16074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-3.png?resize=640%2C90\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-3.png?w=808 808w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-3.png?resize=300%2C42 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-3.png?resize=768%2C108 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-3.png?resize=600%2C85 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<ul>\n<li><strong>nrun\uff1a\u8303\u56f4\u5185\u6bcf\u4e2a\u503c\u7684\u8fed\u4ee3\u6b21\u6570\uff1b<\/strong><\/li>\n<li><strong>options:\u53ef\u4ee5\u8bbe\u7f6e\u662f\u5426\u4fdd\u7559\u6bcf\u6b21\u7684\u8fd0\u7b97\u7ed3\u679c\uff1akeep.all=T\u3002\u4f8b\uff1a.options=list(keep.all=TRUE)<\/strong><\/li>\n<\/ul>\n<p>\u5728\u7ed9\u5927\u5bb6\u8bf4\u660e\u4e86\u6211\u4eec\u5728\u5206\u6790\u4e2d\u7528\u5230\u7684R\u5305\u540e\u5c31\u8981\u5f00\u59cb\u6b63\u5f0f\u4e66\u5199\u5566\uff0c\u6211\u4eec\u524d\u9762\u5df2\u7ecf\u63d0\u5230\u8fd9\u91cc\u6211\u4eec\u4e3e\u7684\u662fNMF\u8fdb\u884c\u805a\u7c7b\u7684\u4f8b\u5b50\uff0c\u8bf4\u5230\u805a\u7c7b\uff0c\u5fc5\u4e0d\u53ef\u5c11\u7684\u4e00\u4e2a\u6b65\u9aa4\u4fbf\u662f\u786e\u5b9a\u5230\u5e95\u8981\u5206\u6210\u51e0\u7c7b\uff0c\u5728\u8fd9\u91cc\u6211\u4eec\u901a\u8fc7\u5176\u4e2d\u7684rank\u53c2\u6570\u8fdb\u884c\u786e\u5b9a\uff0c\u4e0b\u9762\u5c31\u662f\u6211\u4eec\u7684\u4ee3\u7801\u5566\uff1a<\/p>\n<p>n &lt;- 50;<\/p>\n<p>counts &lt;- c(5, 5, 8);<\/p>\n<p>V &lt;- syntheticNMF(n, counts)<\/p>\n<p>\u6211\u4eec\u5728\u8fd9\u91cc\u751f\u6210\u4e00\u4e2a50\u00d718\u7684\u968f\u673a\u77e9\u9635\uff0c\u7136\u540e\u8fdb\u884c\u4e0b\u9762\u7684NMF\u5206\u6790\uff1a<\/p>\n<p>estimate &lt;- nmf(V, rank=2:10, method=&#8221;brunet&#8221;, nrun=5, seed=123)<\/p>\n<p>\u8fd9\u884c\u4ee3\u7801\u662f\u5168\u6587\u7684\u6838\u5fc3\uff01\u53c2\u6570\u5728\u4e0a\u9762\u5df2\u7ecf\u89e3\u91ca\u8fc7\u5566\uff0c\u8fd9\u91cc\u5c31\u4e0d\u8fc7\u591a\u9610\u8ff0\u4e86<\/p>\n<p>plot(estimate)<\/p>\n<p>consensusmap(estimate)<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"329\" class=\"wp-image-16075\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-4.png?resize=640%2C329\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-4.png?w=1920 1920w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-4.png?resize=300%2C154 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-4.png?resize=1024%2C527 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-4.png?resize=768%2C395 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-4.png?resize=1536%2C790 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-4.png?resize=600%2C309 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-4.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u5224\u65ad\u6700\u4f73rank\u503c\u7684\u51c6\u5219\u5c31\u662f\uff0ccophenetic\u503c\u968fK\u53d8\u5316\u7684\u6700\u5927\u53d8\u52a8\u7684\u524d\u70b9\uff0c\u4e0a\u9762\u7ed3\u679c\u4e2dcophenetic\u503c\u5728rank\u4e3a5-6\u65f6\u662f\u7b2c\u4e00\u4e2a\u53d8\u5316\u6700\u5927\u7684\u62d0\u70b9\uff0c\u6240\u4ee5\u9009\u62e9\u6700\u4f73rank\u503c\u4e3a5\u3002<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"329\" class=\"wp-image-16076\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-5.png?resize=640%2C329\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-5.png?w=1920 1920w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-5.png?resize=300%2C154 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-5.png?resize=1024%2C527 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-5.png?resize=768%2C395 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-5.png?resize=1536%2C790 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-5.png?resize=600%2C309 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2023\/10\/word-image-16071-5.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>estimate.rank5 &lt;- nmf(V,5,nrun=10,seed=555555,method = &#8216;brunet&#8217;)<\/p>\n<p>group &lt;- predict(estimate.rank5)<\/p>\n<p>group &lt;- as.data.frame(group)<\/p>\n<p>\u5f53\u786e\u5b9a\u4e86rank5\u4e3a\u6700\u597d\u7684\u805a\u7c7b\u7ed3\u679c\u65f6\uff0c\u53ef\u4ee5\u91cd\u65b0\u4f7f\u7528nmf\u8fdb\u884c\u805a\u7c7b\uff0c\u6700\u540e\u5728group\u4e2d\u67e5\u770b\u5bf9\u5e94\u7684\u5206\u578b\u3002<\/p>\n<p>\u6700\u540e\u662f\u603b\u7ed3\u73af\u8282\u5566\uff0c\u975e\u8d1f\u77e9\u9635\u5206\u89e3 (NMF) \u662f\u4e00\u79cd\u65e0\u76d1\u7763\u5b66\u4e60\u6280\u672f\uff0c\u53ef\u4ee5\u5c06\u4e00\u4e2a\u975e\u8d1f\u77e9\u9635\u5206\u89e3\u4e3a\u4e24\u4e2a\u975e\u8d1f\u77e9\u9635\u7684\u4e58\u79ef\uff0c\u4ece\u800c\u63d0\u53d6\u51fa\u6570\u636e\u7684\u5185\u5728\u7ed3\u6784\u548c\u7279\u5f81\u3002NMF\u6709\u5f88\u591a\u5e94\u7528\uff1a<\/p>\n<ul>\n<li>\u57fa\u56e0\u8868\u8fbe\u6570\u636e\u5206\u6790\uff1aNMF 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