{"id":26293,"date":"2024-01-25T12:19:08","date_gmt":"2024-01-25T04:19:08","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26293"},"modified":"2024-01-25T12:19:11","modified_gmt":"2024-01-25T04:19:11","slug":"%e5%8d%95%e7%bb%86%e8%83%9e%e6%b5%8b%e5%ba%8f%e5%88%86%e6%9e%90%ef%bc%88%e4%ba%94%ef%bc%89r%e5%8c%85seurat%e4%b8%89%e7%a7%8d%e7%ae%97%e6%b3%95%e5%af%b9%e6%95%b0%e6%8d%ae%e8%81%9a%e7%b1%bb%e9%99%8d","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26293","title":{"rendered":"\u5355\u7ec6\u80de\u6d4b\u5e8f\u5206\u6790\uff08\u4e94\uff09R\u5305Seurat\u4e09\u79cd\u7b97\u6cd5\u5bf9\u6570\u636e\u805a\u7c7b\u964d\u7ef4"},"content":{"rendered":"

\u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u4eca\u5929\u7ee7\u7eed\u4ecb\u7ecdR\u5305Seurat\u5355\u7ec6\u80de\u6d4b\u5e8f\u5206\u6790\u3002<\/p>\n

\u4e0a\u4e00\u671f\u6211\u4eec\u7528Seurat\u5bf9\u6570\u636e\u8fdb\u884c\u4e86\u8fdb\u4e00\u6b65\u7684\u8fc7\u6ee4\uff0c\u8fc7\u6ee4\u6389\u4e86\u4e0d\u597d\u7684\u7ec6\u80de\uff08\u6b7b\u7ec6\u80de\uff0c\u7a7a\u7ec6\u80de\uff0c\u591a\u7ec6\u80de\uff09\uff0c\u63d0\u9ad8\u4e86\u6570\u636e\u7684\u8d28\u91cf\uff0c\u5e76\u5bf9\u6570\u636e\u8fdb\u884c\u4e86\u6807\u51c6\u5316\u3002\u4eca\u5929\u6211\u4eec\u5c06\u4f7f\u7528\u4e0d\u540c\u7684\u7b97\u6cd5\u6765\u5bf9\u6570\u636e\u8fdb\u884c\u964d\u7ef4\u3002<\/p>\n

\u4e3a\u4ec0\u4e48\u8981\u505a\u964d\u7ef4\u5462\uff1f<\/h2>\n

\u4eba\u7c7b\u7ec6\u80de\u8ba1\u5212\u6839\u636e\u57fa\u56e0\u8868\u8fbe\u6a21\u5f0f\u4e0d\u540c\u6765\u5206\u7c7b\u7ec6\u80de\u3002\u6709\u7684\u7ec6\u80de\u5206\u5316\u540e\uff0c\u53ea\u4f1a\u8868\u8fbe\u7279\u5b9a\u7684\u57fa\u56e0\uff0c\u4e0d\u4f1a\u518d\u8868\u8fbe\u5176\u4ed6\u7684\u57fa\u56e0\u4e86\uff0c\u6839\u636e\u8868\u8fbe\u7684\u57fa\u56e0\u6765\u5206\u7c7b\u7ec6\u80de\u662f\u53ef\u9760\u7684\u3002<\/p>\n

\u5728\u5c0f\u679c\u6848\u4f8b\u8fd9\u4e2a\u6570\u636e\u96c6\u4e2d\u67092700\u4e2a\u7ec6\u80de\uff0c\u6211\u4eec\u4e0d\u53ef\u80fd\u4e00\u4e2a\u4e00\u4e2a\u53bb\u770b\uff0c\u5b83\u4eec\u5f53\u4e2d\u6709\u5f88\u591a\u8868\u8fbe\u6a21\u5f0f\u662f\u76f8\u4f3c\u7684\uff0c\u6211\u4eec\u53ef\u4ee5\u6839\u636e\u57fa\u56e0\u8868\u8fbe\u6a21\u5f0f\u4e0d\u540c\u6765\u8fdb\u884c\u5206\u7c7b\u3002<\/p>\n

\u4e09\u79cd\u5e38\u7528\u964d\u7ef4\u7b97\u6cd5<\/h2>\n

PCA\u4e3b\u6210\u5206\u5206\u6790<\/h3>\n

\u5176\u539f\u7406\u662f\u901a\u8fc7\u5bf9\u534f\u65b9\u5dee\u77e9\u9635\u8fdb\u884c\u7279\u5f81\u5206\u89e3\uff0c\u4ee5\u5f97\u51fa\u6570\u636e\u7684\u4e3b\u6210\u5206\u4e0e\u5b83\u4eec\u7684\u6743\u503c\uff0c\u5373\u7279\u5f81\u503c\u548c\u7279\u5f81\u5411\u91cf\u3002\u5b83\u4ea7\u751f\u7684\u7ed3\u679c\u53ef\u4ee5\u7406\u89e3\u4e3a\u5bf9\u539f\u6570\u636e\u4e2d\u7684\u65b9\u5dee\u505a\u51fa\u89e3\u91ca\uff1a\u54ea\u4e00\u4e2a\u65b9\u5411\u4e0a\u7684\u6570\u636e\u503c\u5bf9\u65b9\u5dee\u7684\u5f71\u54cd\u6700\u5927\uff1f<\/p>\n

\u901a\u4fd7\u70b9\u8bf4\uff0c\u5c31\u50cf\u9009\u4eba\u5927\u4ee3\u8868\u4e00\u6837\u3002\u6bcf\u4e2a\u9636\u5c42\uff0c\u6bcf\u4e2a\u6c11\u65cf\uff0c\u6bcf\u4e2a\u804c\u4e1a\u9009\u4ee3\u8868\u3002 \u5728\u5355\u7ec6\u80de\u5206\u6790\u4e2d\u5c31\u662f\u5bf9\u7ec6\u80de\u5206\u7ec4\uff0c\u6bcf\u7ec4\u9009\u4ee3\u8868\u6027\u7684\u57fa\u56e0\u9009\u51fa\u6765\u3002<\/p>\n

t-SNE<\/h3>\n

t-SNE\u662f\u4e00\u79cd\u6d41\u884c\u7684\u63a2\u7d22\u9ad8\u7ef4\u6570\u636e\u7684\u65b9\u6cd5\uff0c\u75312008\u5e74\uff0c\u8303\u5fb7\u9a6c\u987f\u548c\u8f9b\u987f\u53d1\u660e\u3002\u5b83\u5177\u6709\u8fd1\u4e4e\u795e\u5947\u7684\u80fd\u529b\uff0c\u53ef\u4ee5\u4ece\u5177\u6709\u6570\u767e\u751a\u81f3\u6570\u5343\u7ef4\u7684\u6570\u636e\u4e2d\u521b\u5efa\u5f15\u4eba\u6ce8\u76ee\u7684\u4e24\u7ef4\u201c\u56fe\u7247\u201d\u3002\u60f3\u7ee7\u7eed\u6df1\u5165\u7406\u89e3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u53bb\u4e0b\u9762\u8fd9\u4e2a\u7f51\u5740\u5b66\u4e60t-SNE\u3002<\/p>\n

How to Use t-SNE Effectively (distill.pub)<\/a><\/p>\n

UMAP<\/h3>\n

UMAP<\/a>\u662fMcInnes\u7b49\u4eba2019\u5e74\u53d1\u660e\u7684\u4e00\u9879\u65b0\u7684\u6570\u636e\u964d\u7ef4\u6280\u672f\u3002\u4e0et-SNE\u76f8\u6bd4\uff0c\u5b83\u5177\u6709\u8bb8\u591a\u4f18\u52bf\uff0c\u6700\u663e\u7740\u7684\u662f\u63d0\u9ad8\u4e86\u901f\u5ea6\u5e76\u66f4\u597d\u5730\u4fdd\u5b58\u4e86\u6570\u636e\u7684\u5168\u5c40\u7ed3\u6784\u3002\u611f\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u53bb\u4e0b\u9762\u8fd9\u4e2a\u7f51\u5740\u4ea4\u4e92\u5f0f\u7406\u89e3UMAP\u7684\u964d\u7ef4\u539f\u7406\u3002<\/p>\n

Understanding UMAP (pair-code.github.io)<\/a><\/p>\n

\u7528Seurat\u5bf9\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u964d\u7ef4<\/h2>\n

\u6211\u4eec\u5bf9\u8fd92700\u4e2a\u7ec6\u80de\u8fdb\u884c\u5206\u7c7b\uff0c\u9996\u5148\u5047\u8bbe\u5206\u621010\u7ec4\u3002<\/p>\n

#\u5c06\u6570\u636e\u6240\u6709\u57fa\u56e0\u540d\u4fdd\u5b58\u5230all.genes\u53d8\u91cf\u4e2d\u3002<\/p>\n

all.genes <- rownames(pbmc)<\/p>\n

#\u9ed8\u8ba4\u5904\u74062000\u4e2a\u57fa\u56e0\uff0c\u6dfb\u52a0features\u5bf9\u6240\u6709\u57fa\u56e0\u8fdb\u884c\u5904\u7406<\/p>\n

pbmc <- ScaleData(pbmc,features = all.genes)<\/p>\n

#\u5982\u679c\u9700\u8981\u79fb\u9664\u4e0d\u60f3\u8981\u7684\u57fa\u56e0\uff0c\u53ef\u4ee5\u6dfb\u52a0vars.to.regress<\/p>\n

pbmc <- ScaleData(pbmc, vars.to.regress = “percent.mt”)<\/p>\n

\u8fd9\u91cc\u79fb\u9664\u6240\u6709\u7684\u7ebf\u7c92\u4f53\u57fa\u56e0\u3002<\/p>\n

#PCA\u5206\u6790\u4e0e\u53ef\u89c6\u5316<\/h2>\n

pbmc <- RunPCA(pbmc,features = VariableFeatures(object = pbmc))<\/p>\n

\u4f7f\u7528RunPCA\u51fd\u6570\u5bf9\u6570\u636epbmc\u8fdb\u884cPCA\u5206\u6790\u3002<\/p>\n

#\u8f93\u51fa\u524d\u4e94\u4e2aPCA\u7ed3\u679c<\/p>\n

print(pbmc[[‘pca’]],dims = 1:9,nfeatures = 5)<\/p>\n

<\/p>\n

#PCA\u53ef\u89c6\u5316\uff0cSeurat\u63d0\u4f9b\u4e09\u4e2a\u51fd\u6570VizDimReduction(), DimPlot(), DimHeatmap()<\/p>\n

VizDimLoadings(pbmc,dims = 1:2,reduction = “pca”)<\/p>\n

<\/p>\n

Pca\u964d\u7ef4\u4e3b\u6210\u52061\u548c2\u7684\u5dee\u5f02\u663e\u8457\u57fa\u56e0<\/p>\n

DimPlot(pbmc,reduction = “pca” )<\/p>\n

<\/p>\n

\u4f7f\u7528PCA\u65b9\u6cd5\u5bf9\u7ec6\u80de\u5206\u7c7b\u3002<\/p>\n

#\u7ed8\u523610\u4e2a<\/p>\n

DimHeatmap(pbmc, dims = 1:10, cells = 500, balanced = TRUE)<\/p>\n

<\/p>\n

\u53ef\u4ee5\u770b\u5230\uff0c\u5230\u4e86\u540e\u9762\u5df2\u7ecf\u4e0d\u80fd\u5f88\u597d\u7684\u5c06\u7ec6\u80de\u533a\u5206\u5f00\u4e86\u3002<\/p>\n

\u786e\u5b9a\u5206\u7ec4\u4e2a\u6570<\/h2>\n

#\u786e\u5b9a\u6570\u636e\u7684\u5206\u7fa4\u4e2a\u6570\uff0c\u6bd4\u8f83\u8017\u65f6<\/p>\n

pbmc <- JackStraw(pbmc,num.replicate = 100)<\/p>\n

pbmc <- ScoreJackStraw(pbmc,dims = 1:20)<\/p>\n

#\u7ed8\u5236\u788e\u77f3\u56fe\uff0c\u786e\u5b9a\u5206\u7fa4\u4e2a\u6570<\/p>\n

JackStrawPlot(pbmc,dims = 1:20)<\/p>\n

<\/p>\n

\u865a\u7ebf\u4ee5\u4e0a\u662f\u7b97\u6cd5\u5efa\u8bae\u5206\u6210\u7684\u7ec4\u6570\u3002<\/p>\n

ElbowPlot(pbmc)<\/p>\n

<\/p>\n

\u4ece\u56fe\u4e2d\u53ef\u4ee5\u770b\u51fa\uff0c10\u4ee5\u540e\u6ca1\u6709\u4ec0\u4e48\u53d8\u5316\u4e86\uff0c\u8bf4\u660e\u63a8\u8350\u5206\u621010\u7ec4\u3002<\/p>\n

\u7ec6\u80de\u805a\u7c7b<\/h2>\n

pbmc <- FindNeighbors(pbmc,dims = 1:10)<\/p>\n

FindNeighbors\u51fd\u6570\u8ba1\u7b97\u7ec6\u80de\u95f4\u8ddd\u79bb\uff0c\u5982\u679c\u4e24\u4e2a\u7ec6\u80de\u8868\u8fbe\u8c31\u8d8a\u76f8\u8fd1\uff0c\u8ddd\u79bb\u8d8a\u5c0f<\/p>\n

pbmc <- FindClusters(pbmc,resolution = 0.5)<\/p>\n

#\u67e5\u770b\u4e0d\u540c\u7ec6\u80de\u7684\u5206\u7fa4<\/p>\n

head(Idents(pbmc),5)<\/p>\n

\u67e5\u770b\u524d5\u4e2a\u7fa4<\/p>\n

<\/p>\n

\u867d\u7136\u6211\u4eec\u8bbe\u7f6edims=10,\u5206\u621010\u7ec4\uff0c\u4f46\u662f\u901a\u8fc7\u805a\u7c7b\u540e\u89c2\u5bdfLevelsLevels\u8bf4\u660e\u7ec6\u80de\u88ab\u5206\u6210\u4e869\u7ec4\u3002<\/p>\n

<\/p>\n

barplot(table(Idents(pbmc)))<\/p>\n

<\/p>\n

\u5217\u51fa\u4e86\u6bcf\u4e2a\u7fa4\u7684\u7ec6\u80de\u6570\u76ee<\/p>\n

t-SNE\u7ec6\u80de\u805a\u7c7b\u4e0e\u53ef\u89c6\u5316<\/h2>\n

pbmc <- RunTSNE(pbmc,dims = 1:10)<\/p>\n

p2 <- DimPlot(pbmc,reduction = “tsne”)<\/p>\n

p2<\/p>\n

<\/p>\n

T-SNE\u5206\u7c7b\u7ed3\u679c\u56fe\u3002<\/p>\n

UMAP\u7ec6\u80de\u805a\u7c7b\u4e0e\u53ef\u89c6\u5316<\/h2>\n

pbmc <- RunUMAP(pbmc,dims = 1:10,label=T)<\/p>\n

<\/p>\n

Reductions\u5b58\u50a8\u7740\u964d\u7ef4\u7684\u7ed3\u679c\uff0c\u7b2c\u4e00\u4e2a\u662fpca\u5206\u6790\u7684\u7ed3\u679c\uff0cumap\u968f\u540e\u88ab\u8ffd\u52a0\u5165\u4e86\u8fdb\u53bb\u3002<\/p>\n

\u6211\u4eec\u53ef\u4ee5\u5c06\u8ba1\u7b97\u597d\u7684UMAP\u7ed3\u679c\u8f93\u51fa\u4e3a\u5355\u72ec\u7684\u6587\u4ef6\uff0c\u7528loupe browse\u67e5\u770b\u3002<\/p>\n

#\u7ed8\u5236UMAP\u56fe<\/p>\n

p1 <- DimPlot(pbmc,reduction = “umap”)<\/p>\n

p1<\/p>\n

<\/p>\n

UMAP\u5206\u7c7b\u7ed3\u679c\u56fe\u3002<\/p>\n

UMAP\u3001t-SNE\u4e0ePCA\u5bf9\u6bd4<\/h2>\n

<\/p>\n

PCA\u5206\u7c7b\u6548\u679c\u6700\u5dee\uff0c\u660e\u663e\u6ca1\u6709\u5206\u5f00\u3002UMAP\u8f83t-SNE\u5206\u7c7b\u6548\u679c\u66f4\u597d\u3002<\/p>\n

\u597d\u60a8\u662f\u5426\u660e\u767d\u4e86\u5462\uff0c\u5982\u679c\u6709\u4e0d\u61c2\u7684\u6765\u548c\u5c0f\u679c\u8ba8\u8bba\u5427~\u4e0b\u671f\u5c0f\u679c\u5c06\u5bf9\u5206\u7c7b\u7684\u7ec6\u80de\u8fdb\u884c\u9274\u5b9a\u4e0e\u5bfb\u627e\u6807\u8bb0\u57fa\u56e0\u3002\u6211\u4eec\u4e0d\u89c1\u4e0d\u6563~<\/p>\n","protected":false},"excerpt":{"rendered":"

\u5927\u5bb6\u597d\uff0c\u5c0f\u679c\u4eca\u5929\u7ee7\u7eed\u4ecb\u7ecdR\u5305Seurat\u5355\u7ec6\u80de\u6d4b\u5e8f\u5206\u6790\u3002 \u4e0a\u4e00\u671f\u6211\u4eec\u7528Seurat\u5bf9\u6570\u636e\u8fdb\u884c\u4e86\u8fdb\u4e00\u6b65\u7684\u8fc7\u6ee4\uff0c\u8fc7 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","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\/26293"}],"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=26293"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26293\/revisions"}],"predecessor-version":[{"id":26307,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26293\/revisions\/26307"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26293"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26293"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26293"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}