{"id":56281,"date":"2024-06-16T17:33:01","date_gmt":"2024-06-16T09:33:01","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=56281"},"modified":"2024-06-16T17:33:01","modified_gmt":"2024-06-16T09:33:01","slug":"%e5%b0%8f%e6%9e%9c%e5%b8%a6%e4%bd%a0%e7%8e%a9%e8%bd%ac%e5%8d%95%e7%bb%86%e8%83%9erna-seq%e6%95%b0%e6%8d%ae%ef%bc%9a%e5%a6%82%e4%bd%95%e5%b7%a7%e7%94%a8clustree%e5%8c%85%e5%88%92%e5%88%86%e8%81%9a-2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=56281","title":{"rendered":"\u5c0f\u679c\u5e26\u4f60\u73a9\u8f6c\u5355\u7ec6\u80deRNA-seq\u6570\u636e\uff1a\u5982\u4f55\u5de7\u7528Clustree\u5305\u5212\u5206\u805a\u7c7b\u4e9a\u7fa4\uff01"},"content":{"rendered":"


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\n<\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 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rel=\"noopener\">#\u79d1\u7814\u4f5c\u56fe<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2812010014583390210#wechat_redirect\" title=\"R\u4ee3\u7801\" target=\"_blank\" rel=\"noopener\">#R\u4ee3\u7801<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2821072943068839938#wechat_redirect\" title=\"\u751f\u4fe1\u7ed8\u56fe\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u7ed8\u56fe<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=2664545260517294084#wechat_redirect\" title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><\/p>\n<\/div>\n<p style=\"text-indent: 0pt;text-align: justify;\" data-mpa-powered-by=\"yiban.io\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013585\" data-ratio=\"0.23333333333333334\" data-s=\"300,640\" data-type=\"jpeg\" data-w=\"1080\" style=\"font-family: \u5b8b\u4f53;font-size: var(--articleFontsize);letter-spacing: 0.578px;text-align: center;height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-17_\u5c0f\u679c\u5e26\u4f60\u73a9\u8f6c\u5355\u7ec6\u80deRNA-seq\u6570\u636e\uff1a\u5982\u4f55\u5de7\u7528Clustree\u5305\u5212\u5206\u805a\u7c7b\u4e9a\u7fa4\uff01\/1_rE2v0O5WiaUDJjgv5bxK2G1ePHyH2g.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAysHY49vPGCraibakiaNq6hQgn8C5MfvVLQGxlNZPEia2PajKAzrE2v0O5WiaUDJjgv5bxK2G1ePHyH2g\/640?wx_fmt=jpeg'\" \/><span style=\"font-size: 15px;font-family: \u5b8b\u4f53;letter-spacing: 0.034em;\">\u5c0f\u4f19\u4f34\u4eec\u5927\u5bb6\u597d\uff0c\u5f88\u5f00\u5fc3\u53c8\u80fd\u548c\u5927\u5bb6\u5206\u4eab\u5206\u4eab\u5c0f\u679c\u5728\u5206\u6790\u5355\u7ec6\u80de\u6570\u636e\u8fc7\u7a0b\u4e2d\u7684\u7ecf\u9a8c\uff0c\u4eca\u5929\u6765\u7ed9\u5927\u5bb6\u8bf4\u8bf4clustree\uff0c\u4e0d\u77e5\u9053\u5927\u5bb6\u8fd8\u8bb0\u4e0d\u8bb0\u5f97\u5c0f\u679c\u4e4b\u524d\u4ecb\u7ecd\u7684Seurat\u5305\uff0c\u8fd9\u4e2a\u5305\u7b97\u662f\u5355\u7ec6\u80deRNA-seq\u5206\u6790\u7684\u59cb\u7956\uff0c\u5b83\u5305\u62ec\u4e86\u6570\u636e\u52a0\u8f7d\u548c\u9884\u5904\u7406\uff0c\u6570\u636e\u8d28\u91cf\u63a7\u5236\uff0c\u5f52\u4e00\u5316\u548c\u6807\u51c6\u5316\uff0c\u964d\u7ef4\uff0c\u805a\u7c7b\uff0c\u7ec6\u80de\u6ce8\u91ca\u7b49\u7b49\u591a\u4e2a\u90e8\u5206\uff0c\u8fd9\u5c31\u4f7f\u5f97Seurat\u5728\u5f53\u524d\u5355\u7ec6\u80de\u6570\u636e\u5206\u6790\u4e2d\u81f3\u5173\u91cd\u8981\uff0c\u56e0\u4e3a\u5b83\u5b9e\u73b0\u4e86\u7aef\u5230\u7aef\u7684\u4e00\u4f53\u5316\u5206\u6790\u6d41\u7a0b\uff0c\u4f46\u662f\u6211\u4eec\u53ef\u4ee5\u4ece\u5b98\u7f51\u4e0a\u770b\u5230\uff0c\u5b83\u5728\u90e8\u5206\u6b65\u9aa4\u4e0a\u662f\u6ca1\u6709\u4f18\u52bf\u7684\uff0c\u6bd4\u5982\u6279\u6b21\u6548\u5e94\u7684\u53bb\u9664\uff0c\u7ec6\u80de\u4e9a\u7fa4\u7684\u6ce8\u91ca\uff0c\u4ee5\u53ca\u6211\u4eec\u4eca\u5929\u60f3\u8bf4\u7684\u5982\u4f55\u5212\u5206\u805a\u7c7b\u4e9a\u7fa4\uff0c\u56e0\u6b64\u73b0\u5728\u4e5f\u51fa\u73b0\u4e86\u5f88\u591a\u4e0e\u5355\u7ec6\u80de\u6709\u5173\u7684\u5305\uff0c\u8fd9\u4e9b\u5305\u662fSeurat\u7684\u8865\u5145\uff0c\u5927\u5bb6\u5206\u6790\u7684\u65f6\u5019\u4e5f\u8981\u5177\u4f53\u95ee\u9898\u5177\u4f53\u5206\u6790\uff0c\u4e0d\u80fd\u5168\u7bc7\u5957Seurat, \u8fd8\u5e94\u8be5\u7d27\u8ddf\u524d\u6cbf\uff0c\u53ca\u65f6\u66f4\u65b0\u81ea\u5df1\u7684\u5206\u6790\u6d41\u7a0b\u5de5\u5177~<br \/><\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u65e2\u7136\u6211\u4eec\u4eca\u5929\u8981\u8bf4\u7684\u805a\u7c7b\u4e9a\u7fa4\uff0c\u90a3\u5fc5\u7136\u8fd8\u662f\u8981\u4ece\u5934\u8bf4\u8d77\uff0c\u8fd9\u6b21\u4f7f\u7528\u7684\u6570\u636e\u662f\u6765\u81ea10XGenomics\u5b98\u7f51\u4e0a\u7684\u5c0f\u9f20\u6570\u636e<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-family: \u5b8b\u4f53;font-size: 15px;letter-spacing: 0.034em;\">\uff08https:\/\/www.10xgenomics.com\/resources\/datasets\/1k-mouse-kidney-nuclei-isolated-with-chromium-nuclei-isolation-kit-3-1-standard\uff09<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-family: \u5b8b\u4f53;font-size: 15px;letter-spacing: 0.034em;\">\u5927\u5bb6\u5148\u8ddf\u7740\u5c0f\u679c\u4e0b\u8f7d\u597d\u6211\u4eec\u5c31\u5f00\u59cb\u5566\uff01<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"kotlin\"><code><span class=\"code-snippet_outer\">library(dplyr)<\/span><\/code><code><span class=\"code-snippet_outer\">library(Seurat)<\/span><\/code><code><span class=\"code-snippet_outer\">library(patchwork)<\/span><\/code><code><span class=\"code-snippet_outer\">library(ggplot2)<\/span><\/code><code><span class=\"code-snippet_outer\">pbmc.<span class=\"code-snippet__keyword\">data<\/span><-Read10X(<span class=\"code-snippet__keyword\">data<\/span>.dir = <span class=\"code-snippet__string\">\".\/ filtered_feature_bc_matrix\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pbmc<-CreateSeuratObject(counts = pbmc.<span class=\"code-snippet__keyword\">data<\/span>,project = <span class=\"code-snippet__string\">\"pbmc3k\"<\/span>,min.cells = <span class=\"code-snippet__number\">3<\/span>,min.features = <span class=\"code-snippet__number\">200<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pbmc[[<span class=\"code-snippet__string\">\"percent.mt\"<\/span>]] <- PercentageFeatureSet(pbmc, pattern = <span class=\"code-snippet__string\">\"^MT-\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pbmc<-subset(pbmc,subset=nFeature_RNA><span class=\"code-snippet__number\">200<\/span> & nFeature_RNA<<span class=\"code-snippet__number\">2500<\/span> & percent.mt<<span class=\"code-snippet__number\">5<\/span>) <\/span><\/code><code><span class=\"code-snippet_outer\">pbmc <- NormalizeData(pbmc, normalization.method = <span class=\"code-snippet__string\">\"LogNormalize\"<\/span>, scale.factor = <span class=\"code-snippet__number\">10000<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">all.genes <- rownames(pbmc)<\/span><\/code><code><span class=\"code-snippet_outer\">pbmc<-FindVariableFeatures(pbmc,selection.method = <span class=\"code-snippet__string\">\"vst\"<\/span>,nfeatures =<span class=\"code-snippet__number\">10<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pbmc <- ScaleData(pbmc, features = all.genes)<\/span><\/code><code><span class=\"code-snippet_outer\">pbmc <- RunPCA(pbmc, features = VariableFeatures(<span class=\"code-snippet__keyword\">object<\/span> = pbmc))<\/span><\/code><code><span class=\"code-snippet_outer\">ElbowPlot(pbmc)<\/span><\/code><code><span class=\"code-snippet_outer\">pbmc <- FindNeighbors(pbmc, dims = <span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pbmc <- FindClusters(pbmc, resolution = <span class=\"code-snippet__number\">0.1<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">pbmc<-RunUMAP(pbmc,dims = <span class=\"code-snippet__number\">1<\/span>:<span class=\"code-snippet__number\">5<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">DimPlot(pbmc,reduction = <span class=\"code-snippet__string\">\"umap\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013591\" data-ratio=\"0.4533333333333333\" data-s=\"300,640\" data-type=\"png\" data-w=\"600\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_R7r7QiarsKDN47BsOA6AicrN6dFcfw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXrqCu1VRhzrlw4hqN8xibnDtVVhdR7r7QiarsKDN47BsOA6AicrN6dFcfw\/640?wx_fmt=png&from=appmsg'\" data-recalc-dims=\"1\" \/><\/p>\n<p><strong><span style=\"font-family: \u5b8b\u4f53;font-size: 15px;letter-spacing: 0.034em;\">\uff08\u987a\u4fbf\u5c0f\u679c\u7ed9\u5927\u5bb6\u9644\u4e0a\u4e24\u5f20Seurat\u7ed3\u679c\u56fe\uff09<\/span><\/strong><span style=\"font-family: \u5b8b\u4f53;font-size: 15px;letter-spacing: 0.034em;\"><\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u9996\u5148\u662f\u5bfc\u5165\u6570\u636e\uff0c\u7136\u540e\u521b\u5efa\u4e00\u4e2aSeurat\u5bf9\u8c61\uff0c\u63a5\u4e0b\u6765\u5bf9\u6570\u636e\u8fdb\u884c\u8d28\u63a7\uff08\u9009\u62e9\u57fa\u56e0\uff0c\u7ec6\u80de\uff0c\u6807\u51c6\u5316..\uff09\uff0c\u4e4b\u540e\u5c31\u8981\u5f00\u59cb\u6b63\u5f0f\u7684\u5206\u6790\u4e86\uff0c\u5148\u5f52\u4e00\u5316\uff0c\u518dPCA\u964d\u7ef4\uff0c\u7136\u540e\u5c31\u8981\u5f00\u59cb\u805a\u7c7b\u5566\uff0c\u90a3\u4e3a\u4ec0\u4e48\u8981\u5148\u964d\u7ef4\u518d\u805a\u7c7b\u5462\uff0c\u90a3\u662f\u56e0\u4e3a\u964d\u7ef4\u53ef\u4ee5\u8ba9\u6570\u636e\u964d\u7ef4\u5230x\u8f74\u548cy\u8f74\u4e0a\u4e24\u4e2a\u7ef4\u5ea6\uff0c\u8fd9\u6837\u4e5f\u66f4\u65b9\u4fbf\u805a\u7c7b\uff0c\u56e0\u6b64RunPCA\u540e\u5c31\u662fFindNeighbors\uff0c\u53c2\u6570\u5982\u679c\u9009\u62e9dim\u4e3a10\uff0c\u5c31\u662f\u572810\u4e2aPCA\u7ef4\u5ea6\u4e0a\u627e\u90bb\u5c45\uff0c\u627e\u5230\u90bb\u5c45\u6839\u636e\u4e00\u4e9b\u56fe\u7684\u7b97\u6cd5\u624d\u80fd\u805a\u7c7b\uff0c\u8bf4\u5230\u8fd9\u91cc\uff0c\u7ec8\u4e8e\u5230\u4e86\u6211\u4eec\u4eca\u5929\u8981\u8bf4\u7684\u51fd\u6570\u4e86\uff01FindClusters(pbmc,resolution=0.1)\uff0c\u8fd9\u662f\u4e00\u4e2a\u805a\u7c7b\u5206\u4e9a\u7fa4\u7684\u5173\u952e\u51fd\u6570\uff0cresolution\u662f\u672c\u6b21\u5185\u5bb9\u7684\u91cd\u70b9\uff01<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u76f8\u4fe1\u5927\u5bb6\u90fd\u77e5\u9053\uff0cResolution\u8d8a\u9ad8\uff0c\u5bf9\u5e94\u7684cluster\u53ef\u80fd\u5c31\u4f1a\u8d8a\u591a\uff0c\u4e9a\u7fa4\u5206\u7684\u8d8a\u591a\u5c31\u4f1a\u5e26\u6765\u4fe1\u606f\u8fc7\u591a\uff0c\u6ca1\u6709\u610f\u4e49\u3002\u800c\u5982\u679cResolution\u8d8a\u5c0f\uff0c\u5219cluster\u8d8a\u5c11\uff0c\u4f1a\u4e22\u5931\u5f88\u591a\u4fe1\u606f\uff0c\u540e\u7eed\u7684\u4e9a\u7fa4\u6ce8\u91ca\u4e5f\u96be\u4ee5\u8fdb\u884c\uff0c\u7531\u6b64\u53ef\u89c1\uff0cresolution\u7684\u8bbe\u7f6e\u5728\u6574\u4e2a\u5b9e\u9a8c\u8fc7\u7a0b\u4e2d\u662f\u5341\u5206\u91cd\u8981\u7684~<\/span>    <\/span><o:page><\/o:page><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u63a5\u4e0b\u6765\u5c0f\u679c\u7ed9\u5927\u5bb6\u5c55\u793a\u4e00\u4e0b\u7a76\u7adf\u662f\u4e0d\u662f\u968f\u7740resolution\u7684\u589e\u9ad8\uff0ccluster\u4e5f\u4f1a\u53d8\u591a\uff0c\u5728\u4ee3\u7801\u4e2d\u6211\u4eec\u5c06resolution\u4ece0.1\u52300.9\u8fdb\u884c\u5faa\u574f\uff0c\u901a\u8fc7dimplot\u6765\u7ed8\u5236\u964d\u7ef4\u7684cluster\u56fe\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"perl\"><code><span class=\"code-snippet_outer\">resolution_values <- se<span class=\"code-snippet__string\">q(0.1, 0.9, by = 0.1)<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">plots <- list() <span class=\"code-snippet__comment\"># \u521b\u5efa\u4e00\u4e2a\u5217\u8868\u6765\u5b58\u50a8\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">for<\/span> (resolution in resolution_values) {<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\"># \u6267\u884c\u805a\u7c7b<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> pbmc <- FindClusters(pbmc, resolution = resolution)<\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\"># \u7ed8\u5236UMAP\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> plot <- DimPlot(pbmc, reduction = <span class=\"code-snippet__string\">\"umap\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"> <span class=\"code-snippet__comment\"># \u6dfb\u52a0\u6807\u9898<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> plot <- plot + ggtitle(paste(<span class=\"code-snippet__string\">\"Resolution =\"<\/span>, resolution))<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"> plots[[<span class=\"code-snippet__keyword\">length<\/span>(plots) + <span class=\"code-snippet__number\">1<\/span>]] <- plot<\/span><\/code><code><span class=\"code-snippet_outer\">}<\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u4f7f\u7528cowplot\u5305\u6392\u5217\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">final_plot <- plot_grid(plotlist = plots, ncol = <span class=\"code-snippet__number\">3<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u663e\u793a\u6700\u7ec8\u7684\u6392\u5217\u56fe<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">final_plot<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-indent: 0pt;text-align: justify;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013581\" data-ratio=\"0.5398148148148149\" data-type=\"png\" data-w=\"1080\" height=\"298.79998779296875\" width=\"553.739990234375\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-17_\u5c0f\u679c\u5e26\u4f60\u73a9\u8f6c\u5355\u7ec6\u80deRNA-seq\u6570\u636e\uff1a\u5982\u4f55\u5de7\u7528Clustree\u5305\u5212\u5206\u805a\u7c7b\u4e9a\u7fa4\uff01\/3_r9pRLgiaiclGEdzvRQ9RORQY77HYTA.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXXaryiaTqtpMYAqsxKRzcdDB9yxur9pRLgiaiclGEdzvRQ9RORQY77HYTA\/640?wx_fmt=png'\" \/><\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013696\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" data-type=\"png\" data-w=\"1080\" style=\"font-size: 15px;letter-spacing: 0.578px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;text-align: center;height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/>\u5728\u672c\u6b21\u7684\u6570\u636e\u4e2d\u867d\u7136\u4e0d\u662f\u5f88\u660e\u663e\uff0c\u4f46\u662f\u4e5f\u53ef\u4ee5\u770b\u5230\u5dee\u5f02\uff0c\u4e00\u5f00\u59cb\u662f3\u4e2acluster\uff0c\u800c\u4e4b\u540e\u53d8\u4e3a\u4e864\u4e2acluster\uff0c\u8fd9\u4e5f\u8bc1\u5b9e\u4e86\u5c0f\u679c\u4e4b\u524d\u8bf4\u7684\u662f\u5bf9\u7684\uff01resolution\u7684\u9009\u62e9\u5341\u5206\u5173\u952e\uff0c\u800c\u6211\u4eec\u8be5\u5982\u4f55\u53bb\u505a\u4e00\u4e2a\u6700\u6070\u5f53\u7684\u9009\u62e9\u5462\uff1f<\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u63a5\u4e0b\u6765\u7ed9\u5927\u5bb6\u770b\u770b\u5982\u4f55\u4f7f\u7528clustree\u5305\u6765\u5224\u65ad\u5e94\u8be5\u5230\u5e95\u53d6\u51e0\u4e2acluster.\u8fd0\u884c\u7684\uff0c\u4ee3\u7801\u5f88\u7b80\u5355\uff1aclustree(pbmc)\u5c31\u53ef\u4ee5\u5566\uff0c\u5982\u679c\u8fd8\u60f3\u52a0\u5165\u4e00\u4e9b\u522b\u7684\u53c2\u6570\u6765\u7f8e\u5316\u8fd9\u4e2a\u56fe\uff0c\u9700\u8981\u5148\u770b\u770bMetadata\u7684colnames:<\/span><\/p>\n<p style=\"text-align: justify;text-indent: 0pt;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013584\" data-ratio=\"0.3231441048034934\" data-type=\"png\" data-w=\"687\" height=\"138.6199951171875\" width=\"428.98004150390625\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-17_\u5c0f\u679c\u5e26\u4f60\u73a9\u8f6c\u5355\u7ec6\u80deRNA-seq\u6570\u636e\uff1a\u5982\u4f55\u5de7\u7528Clustree\u5305\u5212\u5206\u805a\u7c7b\u4e9a\u7fa4\uff01\/5_iaHBd6FRnfSY1whW87BgZxhlCYgneg.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXmg2aFDqr0EQprdgUml9yP05sviaHBd6FRnfSY1whW87BgZxhlCYgneg\/640?wx_fmt=png'\" \/><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"css\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__selector-tag\">clustree<\/span>(<span class=\"code-snippet__selector-tag\">pbmc<\/span>@<span class=\"code-snippet__keyword\">meta<\/span>.<span class=\"code-snippet__keyword\">data<\/span>,<span class=\"code-snippet__keyword\">prefix<\/span> = <span class=\"code-snippet__string\">\"RNA_snn_res.\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-indent: 0pt;text-align: justify;\"><span style=\"font-family: "Times New Roman";font-size: 15px;letter-spacing: 0.034em;\">prefix\u53ef\u4ee5\u9009\u62e9metadata\u4e2d\u7684\u524d\u7f00\u8981\u5bf9\u6bd4\u7684\u5185\u5bb9\uff0c\u6bd4\u5982\u8fd9\u91cc\u662f\u6240\u6709\u7684\u5206\u8fa8\u7387\u3002<\/span><span style=\"font-family: "Times New Roman";font-size: 15px;letter-spacing: 0.034em;\">\u5f53\u7136\uff0c\u8fd8\u6709\u4e00\u4e9b\u5176\u4ed6\u53c2\u6570\uff0c\u5927\u5bb6\u53ef\u4ee5\u81ea\u5df1\u67e5\u4e00\u67e5\uff0c\u5305\u62ec\u989c\u8272\u7b49\u7b49\uff0c\u6700\u540e\u53ef\u4ee5\u7f8e\u5316\u7684\u5f88\u597d\u770b\u54e6<\/span><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;color: rgb(68, 114, 196);font-size: 15px;\"><\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u6700\u540e\u7ed3\u679c\u5982\u4e0b\u56fe\u6240\u793a\uff0c\u90a3\u6211\u4eec\u770b\u7740\u8fd9\u4e2a\u56fe\u8be5\u600e\u4e48\u9009\u62e9\u54ea\u4e2a\u5206\u8fa8\u7387\u5462\uff0c\u9996\u5148\u53ef\u4ee5\u770b\u5230\uff0c\u56fe\u4e0a\u6709\u5f88\u591a\u5708\uff0c\u6bcf\u4e2a\u5708\u7684\u5927\u5c0f\u4ee3\u8868\u5206\u5230\u8fd9\u4e2acluster\u4e2d\u6709\u591a\u5c11\u7ec6\u80de\uff0c\u4e0d\u540c\u7684cluster\u5728\u5708\u4e0a\u90fd\u6709\u6807\u6ce8\uff0c\u800c\u6bcf\u4e2a\u5708\u7684\u989c\u8272\u5219\u662f\u5bf9\u5e94\u7684\u5206\u8fa8\u7387\uff0c\u6bd4\u5982\u5728\u8fd9\u91cc\u603b\u5171\u4ece0.1\u52300.8\u67098\u79cd\u5206\u8fa8\u7387\u3002\u7bad\u5934\u5219\u4ee3\u8868\u8fdb\u4e00\u6b65\u7ec6\u5206\uff0c\u5f53\u6211\u4eec\u9009\u62e9\u7684\u65f6\u5019\uff0c\u66f4\u503e\u5411\u4e8e\u9009\u62e9\u8fdb\u4e00\u6b65\u7ec6\u5206\u7684\u5206\u8fa8\u7387\uff0c\u6bd4\u5982\u7ea2\u8272\u6846\u6807\u6ce8\u7684\u90a3\u6837\uff0c\u4f46\u662f\u84dd\u8272\u6846\u8fd9\u79cd\u4e00\u822c\u5c31\u4e0d\u53ef\u53d6\uff0c\u4e0d\u592a\u53ef\u9760\u3002<\/span> 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data-ratio=\"0.3360655737704918\" data-type=\"jpeg\" data-w=\"244\" height=\"81 .33001708984375\" width=\"243 .4000244140625\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_EicLdPMGCF0zUV3ZkwNlwV7cWQQAmA.jpg?resize=243%2C81\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXLQG8dWGZmyibuK6Z9dFLNFM17TEicLdPMGCF0zUV3ZkwNlwV7cWQQAmA\/640?wx_fmt=jpeg'\" data-recalc-dims=\"1\" \/><\/span><span style=\"left: 0px;margin-left: 116.15pt;margin-top: 155.8pt;width: 91.15pt;height: 70.45pt;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013587\" data-ratio=\"0.7704918032786885\" data-type=\"jpeg\" data-w=\"122\" height=\"93.92999267578125\" width=\"121.54000854492188\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-17_\u5c0f\u679c\u5e26\u4f60\u73a9\u8f6c\u5355\u7ec6\u80deRNA-seq\u6570\u636e\uff1a\u5982\u4f55\u5de7\u7528Clustree\u5305\u5212\u5206\u805a\u7c7b\u4e9a\u7fa4\uff01\/7_6iaviaBianyykDv5v3wXr1Zu2VwEmw.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXaHqibFzA3MH87am7DLOB7wZGDGAe6iaviaBianyykDv5v3wXr1Zu2VwEmw\/640?wx_fmt=jpeg'\" \/><\/span><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013588\" data-ratio=\"0.6135662898252826\" data-type=\"png\" data-w=\"973\" height=\"304 .25\" width=\"495 .8900146484375\" style=\"height: auto !important;\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_9EcEOlN627Bwe6vBoTicF9RxSsY8uA.png?resize=495%2C304\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXabB35ic8IA6xNic8ZWrVZT0HDM69EcEOlN627Bwe6vBoTicF9RxSsY8uA\/640?wx_fmt=png'\" data-recalc-dims=\"1\" \/><\/span><span style=\"font-size: 15px;\">    <br style=\"mso-ignore:vglayout;\" clear=\"all\" \/><\/span><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u90a3\u600e\u4e48\u624d\u80fd\u8ba9\u805a\u7c7b\u7ed3\u679c\u66f4\u6709\u751f\u7269\u5b66\u610f\u4e49\u5462\uff1f\u5c0f\u679c\u5728\u8fd9\u91cc\u5f15\u7528\u4e00\u7bc7\u6709\u5173\u805a\u7c7b\u6811\u7684\u8bba\u6587\u8fdb\u884c\u8bf4\u660e\uff0c\u4e0b\u9762\u8fd9\u5f20\u56fe\u5206\u522b\u4ee5\u56db\u79cd\u7ec6\u80de\u4f5c\u4e3amarker\uff0c\u4ee5\u989c\u8272\u6765\u8868\u793a\u8fd9\u4e9bmarker\u7684\u8868\u8fbe\u91cf\uff0c\u90a3\u600e\u4e48\u8ba9\u8868\u8fbe\u91cf\u6765\u8986\u76d6\u989c\u8272\uff1f\u8fd9\u4e2a\u5c31\u8981\u770b\u4e4b\u524d\u63d0\u5230\u7684\u53c2\u6570\u4e86\uff0c\u5728clustrr\u4e2d\u6709\u4e00\u4e2aexpr\u7684\u5c5e\u6027\uff0c\u53ef\u4ee5\u8bbe\u7f6e\u5b83\u7684\u503c\u6765\u6539\u53d8\u6bcf\u4e2acluster(\u6bcf\u4e2a\u5708)\u7684\u989c\u8272\uff0c\u5f53\u5df2\u77e5\u610f\u4e49\u7684marker\u88ab\u805a\u7c7b\u65f6\uff0cclustree\u4e2d\u663e\u793a\u7684\u6700\u6709\u989c\u8272\u533a\u5206\u5ea6\u7684\u884c\u5c31\u662f\u6211\u4eec\u60f3\u8981\u7684\u5206\u8fa8\u7387\uff0c\u5927\u5bb6\u53ef\u4ee5\u8bd5\u8bd5\u600e\u4e48\u590d\u73b0\u8fd9\u7bc7\u6587\u7ae0\u7684\u8fd9\u5e45\u56fe\uff0c\u8bba\u6587\u540d\u5b57\u4e5f\u653e\u8fd9\u91cc\u5566\uff1aClustering trees: a visualization for evaluating clusterings at multiple resolutions\u3002<\/span>    <\/span><o:page><\/o:page><\/p>\n<p style=\"text-align: justify;\"><span style=\"font-family: "Times New Roman";font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013589\" data-ratio=\"0.6222455403987408\" data-type=\"jpeg\" data-w=\"953\" height=\"258.94000244140625\" width=\"416.0099792480469\" style=\"height: auto !important;\" src=\"\u56fe\u7247\/\u751f\u4fe1\u679c_2023-12-17_\u5c0f\u679c\u5e26\u4f60\u73a9\u8f6c\u5355\u7ec6\u80deRNA-seq\u6570\u636e\uff1a\u5982\u4f55\u5de7\u7528Clustree\u5305\u5212\u5206\u805a\u7c7b\u4e9a\u7fa4\uff01\/9_JNsVl2McNoVib5Cra33C9YGOibCUkw.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXYmba7kFyNbicqIL0XT27YsC3MK4JNsVl2McNoVib5Cra33C9YGOibCUkw\/640?wx_fmt=jpeg'\" \/><\/span><\/p>\n<p style=\"text-align: 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