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class=\"topic\">\n\u6536\u5f55\u4e8e\u8bdd\u9898<\/p>\n<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=2664545260517294084#wechat_redirect\" title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138206666342268940#wechat_redirect\" title=\"\u751f\u4fe1\u5c0f\u767d\u76f8\u5173\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5c0f\u767d\u76f8\u5173<\/a><\/p>\n<\/div>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.2216796875\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_snVaia0ia8A5L1rXZ1xVtIEYJhRYwg-4.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAyOD23lzsibR9jQXL7ibIszDztr50BBOLhoBOyv5vjbFzPuGOYiasnVaia0ia8A5L1rXZ1xVtIEYJhRYwg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1024\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n\u4eb2\u7231\u7684\u679c\u7c89\u513f\u4eec\uff0c\u4f60\u4eec\u597d\uff0c\u5c0f\u679c\u53c8\u6765\u5566\uff01\u5c0f\u679c\u4eca\u5929\u7ed9\u5927\u5bb6\u5e26\u6765\u7684\u5206\u4eab\u662f\u5982\u4f55\u4f7f\u7528Monocle2\u8fdb\u884c\u5355\u7ec6\u80deRNA-seq\u6570\u636e\u5206\u6790\u3002\u8fd9\u4e2a\u5206\u6790\u5de5\u5177\u5728\u5355\u7ec6\u80de\u7814\u7a76\u4e2d\u975e\u5e38\u5b9e\u7528\uff0c\u5c0f\u679c\u5f3a\u70c8\u63a8\u8350\u5c0f\u4f19\u4f34\u4eec\u5b66\u4e60\u3002\u4e00\u8d77\u8ddf\u968f\u5c0f\u679c\u7684\u6b65\u4f10\u5f00\u59cb\u4eca\u5929\u7684\u5b66\u4e60\u5427\uff01<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5074074074074074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_3zibrUqXDUBHvBBaLncwCvMtneNicw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHtBWXicX76aZRWSyI6qoM1ap79Yh3zibrUqXDUBHvBBaLncwCvMtneNicw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><\/p>\nMonocle2\u662f\u4f55\u65b9\u795e\u5723\uff1f<\/strong><\/span><\/p>\nMonocle2\u662f\u4e00\u4e2a\u5f3a\u5927\u7684R\u5305\uff0c\u5b83\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u5206\u6790\u5355\u7ec6\u80deRNA-Seq\u6570\u636e\uff0c\u7814\u7a76\u7ec6\u80de\u7684\u53d1\u80b2\u8f68\u8ff9\u3001\u5206\u5316\u72b6\u6001\u3001\u8f6c\u5f55\u8c03\u63a7\u7279\u5f81\u7b49\u7b49\u3002\u7528\u5b83\uff0c\u4f60\u5c31\u53ef\u4ee5\u50cf\u770b\u7535\u5f71\u4e00\u6837\uff0c\u770b\u5230\u7ec6\u80de\u7684\u751f\u547d\u5386\u7a0b\u3002\u8fc4\u4eca\u4e3a\u6b62\uff0cMonocle\u5df2\u7ecf\u53d1\u5e03\u5230\u4e86\u7b2c\u4e09\u4ee3\uff0c\u800cMonocle2\u662f\u76ee\u524d\u505a\u5355\u7ec6\u80de\u62df\u65f6\u5e8f\u5206\u6790\u6700\u6709\u540d\u7684R\u5305\u3002\u76f8\u8f83\u4e8e\u7b2c\u4e00\u4ee3\u5b83\u6709\u6709\u66f4\u4e30\u5bcc\u7684\u529f\u80fd\uff0c\u800c\u76f8\u8f83\u4ecd\u5728\u6301\u7eed\u5f00\u53d1\u4e2d\u7684Monocle3\u6765\u8bf4\uff0cMonocle2\u66f4\u7a33\u5b9a\u4e14\u66f4\u503e\u5411\u4e8e\u534a\u76d1\u7763\u7684\u5206\u6790\u6a21\u5f0f\uff0c\u53ef\u4ee5\u5229\u7528\u5148\u9a8c\u77e5\u8bc6\u6216\u6807\u8bb0\u57fa\u56e0\u6765\u8fdb\u884c\u4e2a\u6027\u5316\u7684\u8f68\u8ff9\u5206\u6790\u3002<\/span><\/p>\n\u4ec0\u4e48\u662f\u62df\u65f6\u5e8f\u5206\u6790\uff1f<\/strong><\/span><\/p>\n\u62df\u65f6\u5e8f\u5206\u6790\u662f\u4e00\u79cd\u5229\u7528\u5355\u7ec6\u80deRNA-Seq\u6280\u672f\u6765\u6d4b\u91cf\u6bcf\u4e2a\u7ec6\u80de\u7684\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\uff0c\u4ece\u800c\u63ed\u793a\u7ec6\u80de\u7684\u5f02\u8d28\u6027\u3001\u529f\u80fd\u548c\u53d1\u80b2\u8fc7\u7a0b\u7684\u65b9\u6cd5\u3002\u62df\u65f6\u5e8f\u5206\u6790\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u56de\u7b54\u5f88\u591a\u6709\u8da3\u7684\u751f\u7269\u5b66\u95ee\u9898\uff0c\u6bd4\u5982\uff1a<\/span><\/p>\n\u2022\t\u7ec6\u80de\u662f\u5982\u4f55\u4ece\u4e00\u4e2a\u539f\u59cb\u72b6\u6001\u53d1\u80b2\u6210\u4e0d\u540c\u7684\u7c7b\u578b\u548c\u529f\u80fd\u7684\uff1f<\/span><\/p>\n\u2022\t\u7ec6\u80de\u4e4b\u95f4\u6709\u54ea\u4e9b\u5dee\u5f02\u548c\u76f8\u4f3c\u6027\uff1f<\/span><\/p>\n\u2022\t\u7ec6\u80de\u5728\u4e0d\u540c\u7684\u6761\u4ef6\u4e0b\u4f1a\u5982\u4f55\u8868\u8fbe\u4e0d\u540c\u7684\u57fa\u56e0\uff1f<\/span><\/p>\n\u2022\t\u7ec6\u80de\u5728\u4e0d\u540c\u7684\u65f6\u95f4\u70b9\u4f1a\u5982\u4f55\u53d8\u5316\u548c\u6f14\u5316\uff1f<\/span><\/p>\n\u4e3a\u4e86\u56de\u7b54\u8fd9\u4e9b\u95ee\u9898\uff0c\u6211\u4eec\u9700\u8981\u7528\u5230monocle2\u8fd9\u4e2a\u5f3a\u5927\u7684R\u5305\u3002monocle2\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u505a\u4ee5\u4e0b\u51e0\u4ef6\u4e8b\u60c5\uff1a<\/span><\/p>\n\u2022\t\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u8fdb\u884c\u8d28\u91cf\u63a7\u5236\u3001\u6807\u51c6\u5316\u3001\u964d\u7ef4\u548c\u805a\u7c7b\u3002<\/span><\/p>\n\u2022\t\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u8fdb\u884c\u8f68\u8ff9\u5206\u6790\uff0c\u5373\u6839\u636e\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u6765\u6392\u5e8f\u548c\u8fde\u63a5\u6bcf\u4e2a\u7ec6\u80de\uff0c\u6784\u5efa\u51fa\u4e00\u4e2a\u4ee3\u8868\u7ec6\u80de\u53d1\u80b2\u8fc7\u7a0b\u7684\u56fe\u3002<\/span><\/p>\n\u2022\t\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u8fdb\u884c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u5373\u627e\u51fa\u5728\u4e0d\u540c\u8f68\u8ff9\u9636\u6bb5\u6216\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u4e4b\u95f4\u8868\u8fbe\u5dee\u5f02\u663e\u8457\u7684\u57fa\u56e0\u3002<\/span><\/p>\n\u2022\t\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u8fdb\u884c\u53ef\u89c6\u5316\uff0c\u5373\u7528\u5404\u79cd\u56fe\u5f62\u6765\u5c55\u793a\u8f68\u8ff9\u3001\u805a\u7c7b\u3001\u5dee\u5f02\u8868\u8fbe\u7b49\u7ed3\u679c\u3002<\/span><\/p>\n\u542c\u8d77\u6765\u5f88\u9177\u5427\uff1f\u90a3\u4e48\u8ba9\u6211\u4eec\u5f00\u59cb\u5427\uff01\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u5b89\u88c5monocle2\u8fd9\u4e2aR\u5305\u3002<\/span><\/p>\n\u5982\u4f55\u4f7f\u7528Monocle2\uff1f<\/strong><\/span><\/p>\n\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u5728R\u73af\u5883\u4e2d\u5b89\u88c5Monocle2\u5305<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><code>BiocManager::install(\"monocle\")<\/span><\/code><code>library(monocle)<\/span><\/code><\/pre>\n<\/section>\n\u7136\u540e\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u4f7f\u7528Monocle2\u6765\u5206\u6790\u5355\u7ec6\u80de\u6570\u636e\u4e86\u3002<\/span><\/p>\n\u52a0\u8f7d\u5176\u4ed6\u9700\u8981\u7684\u5e93<\/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<\/ul>\n<pre class=\"code-snippet__js\"><code>library(dplyr)<\/span><\/code><code>library(Seurat)<\/span><\/code><code>library(patchwork)<\/span><\/code><\/pre>\n<\/section>\n\u51c6\u5907\u6570\u636e<\/strong><\/span><\/p>\n\u6d4b\u8bd5\u6570\u636e\u6765\u81ea10X Genomics\u514d\u8d39\u63d0\u4f9b\u7684\u5916\u5468\u8840\u5355\u6838\u7ec6\u80de(PBMC)\u6570\u636e\u96c6\u3002\u5c06\u8fd12700\u4e2a\u7ec6\u80de\u3002\u5c0f\u679c\u5df2\u7ecf\u63d0\u524d\u8fdb\u884c\u6807\u51c6\u5316\u5904\u7406\uff0c\u5e76\u6ce8\u91ca\u597d\u4e86\u7ec6\u80de\u7c7b\u578b\uff0c\u50a8\u5b58\u4e3ards\u6587\u4ef6\u3002\u83b7\u53d6\u65b9\u5f0f\u5982\u4e0b\u3002<\/span><\/p>\n\u94fe\u63a5\uff1ahttps:\/\/pan.baidu.com\/s\/1SsrPcXyXX9qb9MtiLlIDRQ?pwd=x3mm<\/span><\/p>\n\u63d0\u53d6\u7801\uff1ax3mm<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code>#\u5bfc\u5165\u6ce8\u91ca\u597d\u7684Seurat\u5bf9\u8c61<\/span><\/code><code>pbmc <- readRDS(\"pbmc3k_test.rds\")<\/span><\/code><code>#\u8fdb\u884c\u9006\u65f6\u5e8f\u5206\u6790\u9700\u8981\u51c6\u5907\u4e09\u4e2a\u6587\u4ef6\uff1a\u8868\u8fbe\u77e9\u9635\u6587\u4ef6(exprs)\u3001\u57fa\u56e0\u5c5e\u6027\u6587\u4ef6(featureData)\u548c\u7ec6#\u80de\u5c5e\u6027\u6587\u4ef6(phenoData)\uff0c\u8fd9\u4e09\u4e2a\u6587\u4ef6\u90fd\u53ef\u4ee5\u4ece\u6211\u4eec\u5904\u7406\u597d\u7684Seurat\u5bf9\u8c61\u4e2d\u83b7\u53d6\u3002<\/span><\/code><code>#\u8868\u8fbe\u77e9\u9635\uff0c\u4ee5\u7a00\u758f\u683c\u5f0f\u5904\u7406\u6570\u636e\uff0c\u53ef\u4ee5\u52a0\u5feb\u8ba1\u7b97\u901f\u5ea6<\/span><\/code><code>exprs <- as(as.matrix(pbmc@assays$RNA@counts), 'sparseMatrix')<\/span><\/code><code>#\u57fa\u56e0\u5c5e\u6027\u6587\u4ef6\uff0c\u8fd9\u662f\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u57fa\u56e0\uff0c\u6bcf\u4e00\u5217\u4ee3\u8868\u4e00\u4e2a\u5c5e\u6027\uff0c\u6bd4\u5982\u57fa\u56e0#\u540d\u3001\u57fa\u56e0\u957f\u5ea6\u7b49\u3002<\/span><\/code><code>featureData <- data.frame(gene_short_name = row.names(pbmc),row.names = row.names(pbmc))<\/span><\/code><code>fd <- new('AnnotatedDataFrame', data = featureData)<\/span><\/code><code>#\u7ec6\u80de\u5c5e\u6027\u6587\u4ef6\uff0c\u8fd9\u662f\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u7ec6\u80de\uff0c\u6bcf\u4e00\u5217\u4ee3\u8868\u4e00\u4e2a\u5c5e\u6027\uff0c\u6bd4\u5982\u7ec6\u80de#\u7c7b\u578b\u3001\u6837\u672c\u6765\u6e90\u7b49\u3002<\/span><\/code><code>phenoData <- pbmc@meta.data<\/span><\/code><code>phenoData$celltype <- pbmc@active.ident<\/span><\/code><code>pd <- new('AnnotatedDataFrame', data = phenoData)<\/span><\/code><\/pre>\n<\/section>\n\u521b\u5efa\u5bf9\u8c61<\/strong><\/span><\/p>\n#\u51c6\u5907\u597d\u4e86\u6211\u4eec\u5c31\u53ef\u4ee5\u5f00\u59cb\u7528monocle2\u7684newCellDataSet\u51fd\u6570\u6765\u521b\u5efa\u4e00\u4e2a\u5355\u7ec6\u80de\u6570\u636e\u5bf9\u8c61\uff0c#\u8fd9\u4e2a\u5bf9\u8c61\u4f1a\u5b58\u50a8\u6240\u6709\u7684\u6570\u636e\u548c\u5206\u6790\u7ed3\u679c\uff0c\u7528\u4e8e\u540e\u7eedmonocle\u5206\u6790<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code>cds<\/span> <- newCellDataSet(exprs,<\/span><\/span><\/code><code>phenoData<\/span> = pd,<\/span><\/span><\/code><code>featureData<\/span> = fd,<\/span><\/span><\/code><code>lowerDetectionLimit<\/span> = 0.5,<\/span><\/span><\/code><code>expressionFamily<\/span> = negbinomial.size())<\/span><\/span><\/code><code>#\u4f30\u8ba1\u5c3a\u5bf8\u56e0\u5b50\u548c\u5206\u6563\u5ea6\uff0c\u8fd9\u4e00\u6b65\u975e\u5e38\u5173\u952e\uff0c\u4e0d\u80fd\u8df3\u8fc7<\/span><\/span><\/code><code>#\u5206\u522b\u6709\u52a9\u4e8e\u6211\u4eec\u5bf9\u8de8\u7ec6\u80de\u6355\u83b7\u7684mRNA\u5dee\u5f02\u8fdb\u884c\u5f52\u4e00\u5316\u548c\u540e\u7eed\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u3002<\/span><\/span><\/code><code>cds<\/span> <- estimateSizeFactors(cds)<\/span><\/span><\/code><code>cds<\/span> <- estimateDispersions(cds)<\/span><\/span><\/code><code>##\u8fc7\u6ee4\u4f4e\u8d28\u91cf\u7ec6\u80de\uff0c\u8fc7\u6ee4\u4f4e\u4e8e1%\u7ec6\u80de\u4e2d\u68c0\u51fa\u7684\u57fa\u56e0<\/span><\/span><\/code><code>cds<\/span> <- detectGenes(cds, min_expr = 0.1)<\/span><\/span><\/code><code>#\u7b5b\u9009\u51fa\u5728\u81f3\u5c1110\u4e2a\u7ec6\u80de\u4e2d\u6709\u8868\u8fbe\u7684\u57fa\u56e0<\/span><\/span><\/code><code>#\u4ece\u5bf9\u8c61\u4e2d\u6392\u9664\u5728\u5c11\u6570\u7ec6\u80de\u4e2d\u8868\u8fbe\u7684\u57fa\u56e0\uff0c\u4ee5\u514d\u6d6a\u8d39CPU\u65f6\u95f4\u5206\u6790\u5b83\u4eec\u7684\u5dee\u5f02\u8868\u8fbe\u3002<\/span><\/span><\/code><code>expressed_genes<\/span> <- row.names(subset(fData(cds),<\/span><\/span><\/code><code>num_cells_expressed<\/span> >= 10))<\/span><\/span><\/code><\/pre>\n<\/section>\n\u7ec6\u80de\u5206\u7c7b<\/strong><\/span><\/p>\nMonocle \u63d0\u4f9b\u4e86\u4e00\u4e2a\u7b80\u5355\u7684\u7cfb\u7edf\uff0c\u7528\u4e8e\u6839\u636e\u6211\u4eec\u9009\u62e9\u7684\u6807\u8bb0\u57fa\u56e0\u7684\u8868\u8fbe\u6765\u9274\u5b9a#\u7ec6\u80de\u3002\u4f46\u662f\u672f\u4e1a\u6709\u4e13\u653b\uff0cmonocle\u6bd5\u7adf\u4e0d\u662f\u4e13\u95e8\u4f5c\u7ec6\u80de\u9274\u5b9a\u7684\u8f6f\u4ef6\uff0c\u5c0f\u679c\u8fd8\u662f\u5efa\u8bae\u5148\u505a\u597d\u7ec6#\u80de\u6ce8\u91ca\u4ee5\u540e\u518d\u5bfc\u5165monocle\u8fdb\u884c\u5206\u6790\uff0c\u8d34\u5fc3\u7684\u5c0f\u679c\u4eca\u5929\u5c31\u63d0\u524d\u5904\u7406\u4e86\uff0c\u543c\u543c~<\/span><\/p>\n\u6784\u5efa\u5355\u7ec6\u80de\u8f68\u8ff9<\/strong><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code># \u7b2c1\u6b65\uff1a\u9009\u62e9\u5b9a\u4e49\u7ec6\u80de\u8fdb\u5c55\u7684\u57fa\u56e0<\/span><\/code><code>#\u5bf9cds\u5bf9\u8c61\u4e2d\u7684expressed_genes\u57fa\u56e0\u8fdb\u884c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u5e76\u5c06\u7ed3\u679c\u8d4b\u503c\u7ed9diff\u53d8\u91cf\u3002~ celltype\u8868\u793a\u6211\u4eec\u60f3\u8981\u6bd4\u8f83\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u4e4b\u95f4\u7684\u57fa\u56e0\u8868\u8fbe\u5dee\u5f02<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>diff <- differentialGeneTest(cds[expressed_genes,],<\/span><\/code><code>fullModelFormulaStr=\"~celltype\",<\/span><\/code><code>cores=1)<\/span><\/code><code>#\u627e\u51fa\u90a3\u4e9b\u5728\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u4e4b\u95f4\u6709\u663e\u8457\u5dee\u5f02\u8868\u8fbe\u7684\u57fa\u56e0\uff0c\u4ee5\u7528\u4e8e\u7ec6\u80de\u6392\u5e8f\u3002<\/span><\/code><code>ordergene <- rownames(subset(diff, qval < 0.01))<\/span><\/code><code>#\u6807\u8bb0\u4e3a\u7528\u4e8e\u7ec6\u80de\u6392\u5e8f\u7684\u57fa\u56e0<\/span><\/code><code>#\u4e00\u65e6\u6211\u4eec\u6709\u4e86\u7528\u4e8e\u6392\u5e8f\u7684\u57fa\u56e0 ID \u5217\u8868\uff0c\u6211\u4eec\u9700\u8981\u5728 cds\u5bf9\u8c61\u4e2d\u8bbe\u7f6e\u5b83\u4eec\u3002<\/span><\/code><code>cds <- setOrderingFilter(cds, ordergene)<\/span><\/code><code>#\u5176\u4e2d\u9ed1\u70b9\u5c31\u662f\u540e\u9762\u6784\u5efa\u53d1\u80b2\u8f68\u8ff9\u9700\u8981\u7684\u57fa\u56e0<\/span><\/code><code>plot_ordering_genes(cds)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.869811320754717\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_caPEYfpsWD1xkxTE9mLf13uibL0ZBQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHkfDf2rLulHMeBLy6micNGFVsv0caPEYfpsWD1xkxTE9mLf13uibL0ZBQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"530\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code>#\u7b2c\u4e8c\u6b65: \u964d\u4f4e\u6570\u636e\u7ef4\u5ea6<\/span><\/code><code>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u964d\u7ef4\u5230\u4e8c\u7ef4\u7a7a\u95f4\uff0c\u6211\u4eec\u5c06\u80fd\u591f\u5728Monocle\u7ec6\u80de\u6392\u5e8f\u65f6\u8fdb\u884c\u53ef\u89c6\u5316\u548c\u89e3\u91ca\u3002<\/span><\/code><code>cds <- reduceDimension(cds, max_components = 2,<\/span><\/code><code>method = 'DDRTree')<\/span><\/code><code># \u7b2c\u4e09\u6b65: \u6cbf\u8f68\u8ff9\u5bf9\u7ec6\u80de\u8fdb\u884c\u6392\u5e8f<\/span><\/code><code>cds <- orderCells(cds)<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>#\u6309Pseudotime\u5c55\u793a\uff0cPseudotime\u662f\u4e00\u79cd\u7528\u6765\u8861\u91cf\u6bcf\u4e2a\u7ec6\u80de\u5728\u53d1\u80b2\u8f68\u8ff9\u4e2d\u7684\u76f8\u5bf9\u4f4d\u7f6e\u6216\u865a\u62df\u65f6\u95f4\u7684\u6307\u6807\uff0c\u5b83\u53cd\u6620\u4e86\u6bcf\u4e2a\u7ec6\u80de\u7684\u53d1\u80b2\u8fdb\u7a0b\u548c\u5206\u5316\u72b6\u6001\u3002Pseudotime\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u53d1\u73b0\u90a3\u4e9b\u968f\u7740\u53d1\u80b2\u8fc7\u7a0b\u800c\u53d8\u5316\u7684\u57fa\u56e0\u6216\u8f6c\u5f55\u56e0\u5b50\u3002<\/span><\/code><code>plot_cell_trajectory(cds,color_by=\"Pseudotime\", size=1,show_backbone=TRUE)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.869811320754717\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_fJ2oJNUyuy8HCDGB3xzSFbqyn61Fdw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHl3gDr0nfNlN9rtiaKicjEBYBpdfJ2oJNUyuy8HCDGB3xzSFbqyn61Fdw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"530\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>#\u6309\u7ec6\u80de\u7c7b\u578b\u5c55\u793a<\/span><\/code><code>plot_cell_trajectory(cds,color_by=\"celltype\", size=1,show_backbone=TRUE)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.869811320754717\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_nqIZu4naH041DvyCQUnOCic8mibnZQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHtBGnorCXqAiaGuW0NRl8f3OPApLnqIZu4naH041DvyCQUnOCic8mibnZQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"530\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>#\u6309state\u5c55\u793a\uff0c\u8fd8\u53ef\u4ee5\u4f5c\u5206\u9762\u56fe<\/span><\/code><code>plot_cell_trajectory(cds, color_by = \"State\",size=1,show_backbone=TRUE)<\/span><\/code><code>plot_cell_trajectory(cds, color_by = \"State\") + facet_wrap(\"~State\", nrow = 1)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.869811320754717\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_ZZV4VwJu7ewicSYqqiagkKRniaTD4A.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHOqDhhaSSPznysrlTgjV9XGDAYV1ZZV4VwJu7ewicSYqqiagkKRniaTD4A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"530\" data-recalc-dims=\"1\" \/><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.48526315789473684\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_5SZ3oeUXGHOmof4hAY69QhgaNUxfgw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHEXECvXOGB9keCnLJG1Wk7B805SZ3oeUXGHOmof4hAY69QhgaNUxfgw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"950\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code>#\u6309\u6ce8\u91ca\u4e4b\u524d\u7684\u5206\u7fa4\u7ed3\u679c\u5c55\u793a<\/span><\/code><code>plot_cell_trajectory(cds, color_by = \"seurat_clusters\")<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.869811320754717\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_V9EDbekfwrFtoQVd8aSFkWfdGrjPOg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHWsNTliaGMPrv45Pth4tTRGOmHV9EDbekfwrFtoQVd8aSFkWfdGrjPOg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"530\" data-recalc-dims=\"1\" \/><\/p>\n\u4eca\u5929\uff0c\u5c0f\u679c\u5c31\u5e26\u5927\u5bb6\u63a2\u7d22\u5230\u8fd9\u91cc\uff01\u5e0c\u671b\u4f60\u5df2\u7ecf\u7b80\u5355\u4e86\u89e3\u5982\u4f55\u4f7f\u7528Monocle2\u6765\u89c2\u5bdf\u5355\u7ec6\u80de\u7684\u53d1\u5c55\u5386\u7a0b\u3002\u5982\u679c\u6709\u4ec0\u4e48\u95ee\u9898\u6216\u8005\u7591\u95ee\uff0c\u6b22\u8fce\u5728\u8bc4\u8bba\u533a\u7559\u8a00\uff0c\u5c0f\u679c\u4f1a\u79d2\u56de\u7684\u54e6\u3002\u5982\u679c\u4f60\u89c9\u5f97\u4eca\u5929\u7684\u5185\u5bb9\u6709\u7528\uff0c\u522b\u5fd8\u4e86\u70b9\u8d5e\u548c\u5206\u4eab\u54e6\uff0c\u8fd9\u662f\u5bf9\u5c0f\u679c\u7684\u6700\u5927\u652f\u6301\uff01\u6211\u4eec\u4e0b\u6b21\u518d\u89c1\uff01<\/strong><\/span><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247493633&idx=1&sn=2263dfe7572c0bcf6816c2c1a37d79de&chksm=cf7f78c4f808f1d2209321d6ace39fde5fa60c0691b56f88eac21916f5a2872ce8ee345f1d5f&scene=21#wechat_redirect\" 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{"id":60472,"date":"2024-06-17T11:26:24","date_gmt":"2024-06-17T03:26:24","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60472"},"modified":"2024-06-17T11:26:24","modified_gmt":"2024-06-17T03:26:24","slug":"%e4%b8%80%e5%ad%a6%e5%b0%b1%e4%bc%9a%e7%9a%84%e6%8b%9f%e6%97%b6%e5%ba%8f%e5%88%86%e6%9e%90%ef%bc%9a%e7%94%a8monocle2%e6%b4%9e%e5%af%9f%e7%bb%86%e8%83%9e%e5%8f%91%e8%82%b2","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=60472","title":{"rendered":"\u4e00\u5b66\u5c31\u4f1a\u7684\u62df\u65f6\u5e8f\u5206\u6790\uff1a\u7528Monocle2\u6d1e\u5bdf\u7ec6\u80de\u53d1\u80b2"},"content":{"rendered":"

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60px}.rich_media_area_extra{padding:0 60px 21px 60px}}@media (min-width:1024px){.rich_media_area_primary_inner,.rich_media_area_extra_inner,body{max-width:677px;margin-left:auto;margin-right:auto}.rich_media_area_primary{padding-top:32px}}.rich_media{padding:20px;overflow:hidden;}.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}@media screen and (min-width:1024px){.rich_media_area_primary_inner,.rich_media_area_extra_inner{max-width:677px;margin-left:auto;margin-right:auto}.rich_media_area_primary{padding-top:32px}}.rich_media_content{overflow:hidden;color:#333;font-size:17px;word-wrap:break-word;-webkit-hyphens:auto;-ms-hyphens:auto;hyphens:auto;text-align:justify;position:relative;z-index:0}.rich_media_content *{max-width:100%!important;box-sizing:border-box!important;-webkit-box-sizing:border-box!important;word-wrap:break-word!important}.rich_media_content p{clear:both;min-height:1em}.rich_media_content em{font-style:italic}.rich_media_content fieldset{min-width:0}.rich_media_content .list-paddingleft-1,.rich_media_content .list-paddingleft-2,.rich_media_content .list-paddingleft-3{padding-left:2.2em}.rich_media_content .list-paddingleft-1 .list-paddingleft-2,.rich_media_content .list-paddingleft-2 .list-paddingleft-2,.rich_media_content .list-paddingleft-3 .list-paddingleft-2{padding-left:30px}.rich_media_content .list-paddingleft-1{padding-left:1.2em}.rich_media_content .list-paddingleft-3{padding-left:3.2em}.rich_media_content .code-snippet,.rich_media_content .code-snippet__fix{max-width:1000%!important}.rich_media_content .code-snippet *,.rich_media_content .code-snippet__fix *{max-width:1000%!important}.rich_media_title{font-size:22px;line-height:1.4;margin-bottom:13px;padding-bottom:13px;border-bottom:1px solid #e7e7eb;}@supports(-webkit-overflow-scrolling:touch){.rich_media_title{font-weight:700}}.rich_media_meta{display:inline-block;vertical-align:middle;padding:0 0 10px 0;font-size:15px;-webkit-tap-highlight-color:rgba(0,0,0,0)}.rich_media_meta.icon_appmsg_tag{margin-right:0px}.rich_media_meta.meta_tag_text{margin-right:0}.rich_media_meta_list em{font-style:normal}.rich_media_meta_text{color:#a5a5a5;}p{margin:0;}.msgBox{margin-top:20px;padding-top:20px;padding-left:50px;overflow:hidden;border-top:2px dashed #09a2ff;}.msg{padding-top:7px;clear:both;}.msgBody{float:right;width:100%;margin-left:55px;padding-bottom:15px;border-bottom:1px dashed #e0e0e0;}.userHeadImg{float:left;margin-left:-50px;}.userHeadImg img{width:40px;height:40px;margin-right:10px;border-radius:3px;}.userName{color:#888888;line-height:24px;font-size:14px;margin:5px 0 5px 0;height:24px;}.replyBody,.autherBody{color:#565656;font-size:15px;}.replyIcon{border-left:4px solid #33ab01;margin-right:5px;}.ad{text-decoration:none;color:#d6d4d4;font-size:12px;}.msgBodyReply{padding-top:5px;}.userName span{float:right;color:#afafaf;font-size:14px;}code{text-align:left;font-size:14px;display:block;white-space:pre;display:-webkit-box;display:-webkit-flex;display:flex;position:relative;}.code-snippet__fix{font-size:14px;margin:10px 0;display:block;color:#333;position:relative;background-color:rgba(0,0,0,0.03);border:1px solid #f0f0f0;border-radius:2px;display:-webkit-box;display:-webkit-flex;display:flex;padding-left:25px;line-height:26px}.code-snippet__fix code{text-align:left;font-size:14px;display:block;white-space:pre;display:-webkit-box;display:-webkit-flex;display:flex;position:relative;font-family:Consolas,\"Liberation Mono\",Menlo,Courier,monospace}.code-snippet__comment,.code-snippet__quote{color:#afafaf;font-style:italic}.code-snippet__keyword,.code-snippet__selector-tag,.code-snippet__subst{color:#ca7d37}.code-snippet__number,.code-snippet__literal,.code-snippet__variable,.code-snippet__template-variable,.code-snippet__tag .code-snippet__attr{color:#0e9ce5}.code-snippet__string,.code-snippet__doctag{color:#d14}.code-snippet__title,.code-snippet__section,.code-snippet__selector-id{color:#d14}.code-snippet__subst{font-weight:normal}.code-snippet__type,.code-snippet__class 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0;align-items:center}.flex_bd{padding-left:14px;}.account_nickname{display:inline-block;vertical-align:middle;line-height:1.2;color:#576b95;font-size:14px}.account_desc{overflow:hidden;text-overflow:ellipsis;display:-webkit-box;-webkit-box-orient:vertical;-webkit-line-clamp:1;color:rgba(0,0,0,0.3);font-size:14px;line-height:1.2;padding-top:.4em}.msg_source_url{text-align:left;word-break:break-all;margin-top:20px;}.msg_source_url a{padding-right:10px;}.msg_source_url .url_text{color:#a8a8a8;}.video-desc{font-size:14px;margin-top:15px;color:#6c6c6c;}.msg_source_url{text-align:left;}.original_primary_card_tips{color:rgba(0,0,0,0.3);line-height:1.4;font-size:15px;}.weui-flex__item{margin-bottom:20px;padding:20px 16px;margin-top:16px;line-height:1.4;align-items:center;background-color:#f7f7f7;border-radius:8px;position:relative;}.original_primary_desc{color:rgba(0,0,0,0.5);font-size:14px;padding-top:4px;width:auto;overflow:hidden;text-overflow:ellipsis;}.msgBodyReplyList{border-top:1px solid #e1e1e1;margin-top:10px;}.msgBodyReplyListTop{border-top:0;}.reply_like_num{float:right;font-size:14px;color:#c7c7c7;}.msgData{margin-top:20px;color:#626262;}.msgData span{font-size:14px;padding-right:15px;}.msgData .likes{float:right;padding-right:0;}.js_text_content p{font-size:18px;}.rich_media_meta_link{font-size:15px;}blockquote {padding-left: 10px;border-left: 3px solid #dbdbdb;color: rgba(0,0,0,0.5);font-size: 15px;padding-top: 4px;margin: 1em 0;}.video_iframe{width:500px;height:400px;}.blockquote_info{color:#b5b5b5;margin-top:10px;}#copyright_logo{color:#bdbdbd;}.rich_media_meta_list{margin-bottom:10px;}.reprint{background:#efefef;border-radius:5px;padding:8px;color:#1f1f1f;}.reprint a{word-break:break-all;}.topic{color:#8e8e8e;background:#f7f7f7;border-radius:5px;padding:10px 8px;}.topic a{padding-right:5px;}.topic p{margin-bottom:5px;}\n<\/style>\n<link href=\"https:\/\/www.juyifx.cn\/config\/css\/wxArticle.css\" rel=\"stylesheet\"\/>\n<\/head><script>\nvar data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"\u4e00\u5b66\u5c31\u4f1a\u7684\u62df\u65f6\u5e8f\u5206\u6790\uff1a\u7528Monocle2\u6d1e\u5bdf\u7ec6\u80de\u53d1\u80b2\",\"time\":\"2023-11-03 19:00:58\",\"timeStamp\":\"1699009258\"};\n<\/script> \n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247495008&idx=1&sn=1df9d32feb4e54b0f54c4301d660c904&chksm=cf7f7da5f808f4b353a553b00a22f03091d214c53533785d5415038409d0f2d88e6ee8510787#rd\" target=\"_blank\" rel=\"noopener\">\u4e00\u5b66\u5c31\u4f1a\u7684\u62df\u65f6\u5e8f\u5206\u6790\uff1a\u7528Monocle2\u6d1e\u5bdf\u7ec6\u80de\u53d1\u80b2<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\">\u539f\u521b <\/span>\u5c0f\u679c <\/span><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span>2023-11-03 19:00:58<\/em><\/div>\n<content><\/p>\n<div class=\"topic\">\n\u6536\u5f55\u4e8e\u8bdd\u9898<\/p>\n<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=2664545260517294084#wechat_redirect\" title=\"\u751f\u4fe1\u5b9e\u64cd\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5b9e\u64cd<\/a><a href=\"https:\/\/mp.weixin.qq.com\/mp\/appmsgalbum?__biz=Mzg3OTg3MjQyNg==&action=getalbum&album_id=3138206666342268940#wechat_redirect\" title=\"\u751f\u4fe1\u5c0f\u767d\u76f8\u5173\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u5c0f\u767d\u76f8\u5173<\/a><\/p>\n<\/div>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.2216796875\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_snVaia0ia8A5L1rXZ1xVtIEYJhRYwg-4.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAyOD23lzsibR9jQXL7ibIszDztr50BBOLhoBOyv5vjbFzPuGOYiasnVaia0ia8A5L1rXZ1xVtIEYJhRYwg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1024\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n\u4eb2\u7231\u7684\u679c\u7c89\u513f\u4eec\uff0c\u4f60\u4eec\u597d\uff0c\u5c0f\u679c\u53c8\u6765\u5566\uff01\u5c0f\u679c\u4eca\u5929\u7ed9\u5927\u5bb6\u5e26\u6765\u7684\u5206\u4eab\u662f\u5982\u4f55\u4f7f\u7528Monocle2\u8fdb\u884c\u5355\u7ec6\u80deRNA-seq\u6570\u636e\u5206\u6790\u3002\u8fd9\u4e2a\u5206\u6790\u5de5\u5177\u5728\u5355\u7ec6\u80de\u7814\u7a76\u4e2d\u975e\u5e38\u5b9e\u7528\uff0c\u5c0f\u679c\u5f3a\u70c8\u63a8\u8350\u5c0f\u4f19\u4f34\u4eec\u5b66\u4e60\u3002\u4e00\u8d77\u8ddf\u968f\u5c0f\u679c\u7684\u6b65\u4f10\u5f00\u59cb\u4eca\u5929\u7684\u5b66\u4e60\u5427\uff01<\/span><\/p>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.5074074074074074\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_3zibrUqXDUBHvBBaLncwCvMtneNicw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHtBWXicX76aZRWSyI6qoM1ap79Yh3zibrUqXDUBHvBBaLncwCvMtneNicw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" data-recalc-dims=\"1\" \/><\/p>\nMonocle2\u662f\u4f55\u65b9\u795e\u5723\uff1f<\/strong><\/span><\/p>\nMonocle2\u662f\u4e00\u4e2a\u5f3a\u5927\u7684R\u5305\uff0c\u5b83\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u5206\u6790\u5355\u7ec6\u80deRNA-Seq\u6570\u636e\uff0c\u7814\u7a76\u7ec6\u80de\u7684\u53d1\u80b2\u8f68\u8ff9\u3001\u5206\u5316\u72b6\u6001\u3001\u8f6c\u5f55\u8c03\u63a7\u7279\u5f81\u7b49\u7b49\u3002\u7528\u5b83\uff0c\u4f60\u5c31\u53ef\u4ee5\u50cf\u770b\u7535\u5f71\u4e00\u6837\uff0c\u770b\u5230\u7ec6\u80de\u7684\u751f\u547d\u5386\u7a0b\u3002\u8fc4\u4eca\u4e3a\u6b62\uff0cMonocle\u5df2\u7ecf\u53d1\u5e03\u5230\u4e86\u7b2c\u4e09\u4ee3\uff0c\u800cMonocle2\u662f\u76ee\u524d\u505a\u5355\u7ec6\u80de\u62df\u65f6\u5e8f\u5206\u6790\u6700\u6709\u540d\u7684R\u5305\u3002\u76f8\u8f83\u4e8e\u7b2c\u4e00\u4ee3\u5b83\u6709\u6709\u66f4\u4e30\u5bcc\u7684\u529f\u80fd\uff0c\u800c\u76f8\u8f83\u4ecd\u5728\u6301\u7eed\u5f00\u53d1\u4e2d\u7684Monocle3\u6765\u8bf4\uff0cMonocle2\u66f4\u7a33\u5b9a\u4e14\u66f4\u503e\u5411\u4e8e\u534a\u76d1\u7763\u7684\u5206\u6790\u6a21\u5f0f\uff0c\u53ef\u4ee5\u5229\u7528\u5148\u9a8c\u77e5\u8bc6\u6216\u6807\u8bb0\u57fa\u56e0\u6765\u8fdb\u884c\u4e2a\u6027\u5316\u7684\u8f68\u8ff9\u5206\u6790\u3002<\/span><\/p>\n\u4ec0\u4e48\u662f\u62df\u65f6\u5e8f\u5206\u6790\uff1f<\/strong><\/span><\/p>\n\u62df\u65f6\u5e8f\u5206\u6790\u662f\u4e00\u79cd\u5229\u7528\u5355\u7ec6\u80deRNA-Seq\u6280\u672f\u6765\u6d4b\u91cf\u6bcf\u4e2a\u7ec6\u80de\u7684\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\uff0c\u4ece\u800c\u63ed\u793a\u7ec6\u80de\u7684\u5f02\u8d28\u6027\u3001\u529f\u80fd\u548c\u53d1\u80b2\u8fc7\u7a0b\u7684\u65b9\u6cd5\u3002\u62df\u65f6\u5e8f\u5206\u6790\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u56de\u7b54\u5f88\u591a\u6709\u8da3\u7684\u751f\u7269\u5b66\u95ee\u9898\uff0c\u6bd4\u5982\uff1a<\/span><\/p>\n\u2022\t\u7ec6\u80de\u662f\u5982\u4f55\u4ece\u4e00\u4e2a\u539f\u59cb\u72b6\u6001\u53d1\u80b2\u6210\u4e0d\u540c\u7684\u7c7b\u578b\u548c\u529f\u80fd\u7684\uff1f<\/span><\/p>\n\u2022\t\u7ec6\u80de\u4e4b\u95f4\u6709\u54ea\u4e9b\u5dee\u5f02\u548c\u76f8\u4f3c\u6027\uff1f<\/span><\/p>\n\u2022\t\u7ec6\u80de\u5728\u4e0d\u540c\u7684\u6761\u4ef6\u4e0b\u4f1a\u5982\u4f55\u8868\u8fbe\u4e0d\u540c\u7684\u57fa\u56e0\uff1f<\/span><\/p>\n\u2022\t\u7ec6\u80de\u5728\u4e0d\u540c\u7684\u65f6\u95f4\u70b9\u4f1a\u5982\u4f55\u53d8\u5316\u548c\u6f14\u5316\uff1f<\/span><\/p>\n\u4e3a\u4e86\u56de\u7b54\u8fd9\u4e9b\u95ee\u9898\uff0c\u6211\u4eec\u9700\u8981\u7528\u5230monocle2\u8fd9\u4e2a\u5f3a\u5927\u7684R\u5305\u3002monocle2\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u505a\u4ee5\u4e0b\u51e0\u4ef6\u4e8b\u60c5\uff1a<\/span><\/p>\n\u2022\t\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u8fdb\u884c\u8d28\u91cf\u63a7\u5236\u3001\u6807\u51c6\u5316\u3001\u964d\u7ef4\u548c\u805a\u7c7b\u3002<\/span><\/p>\n\u2022\t\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u8fdb\u884c\u8f68\u8ff9\u5206\u6790\uff0c\u5373\u6839\u636e\u57fa\u56e0\u8868\u8fbe\u6c34\u5e73\u6765\u6392\u5e8f\u548c\u8fde\u63a5\u6bcf\u4e2a\u7ec6\u80de\uff0c\u6784\u5efa\u51fa\u4e00\u4e2a\u4ee3\u8868\u7ec6\u80de\u53d1\u80b2\u8fc7\u7a0b\u7684\u56fe\u3002<\/span><\/p>\n\u2022\t\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u8fdb\u884c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u5373\u627e\u51fa\u5728\u4e0d\u540c\u8f68\u8ff9\u9636\u6bb5\u6216\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u4e4b\u95f4\u8868\u8fbe\u5dee\u5f02\u663e\u8457\u7684\u57fa\u56e0\u3002<\/span><\/p>\n\u2022\t\u5bf9\u5355\u7ec6\u80de\u6570\u636e\u8fdb\u884c\u53ef\u89c6\u5316\uff0c\u5373\u7528\u5404\u79cd\u56fe\u5f62\u6765\u5c55\u793a\u8f68\u8ff9\u3001\u805a\u7c7b\u3001\u5dee\u5f02\u8868\u8fbe\u7b49\u7ed3\u679c\u3002<\/span><\/p>\n\u542c\u8d77\u6765\u5f88\u9177\u5427\uff1f\u90a3\u4e48\u8ba9\u6211\u4eec\u5f00\u59cb\u5427\uff01\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u5b89\u88c5monocle2\u8fd9\u4e2aR\u5305\u3002<\/span><\/p>\n\u5982\u4f55\u4f7f\u7528Monocle2\uff1f<\/strong><\/span><\/p>\n\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u5728R\u73af\u5883\u4e2d\u5b89\u88c5Monocle2\u5305<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"sql\"><code>BiocManager::install(\"monocle\")<\/span><\/code><code>library(monocle)<\/span><\/code><\/pre>\n<\/section>\n\u7136\u540e\uff0c\u6211\u4eec\u5c31\u53ef\u4ee5\u4f7f\u7528Monocle2\u6765\u5206\u6790\u5355\u7ec6\u80de\u6570\u636e\u4e86\u3002<\/span><\/p>\n\u52a0\u8f7d\u5176\u4ed6\u9700\u8981\u7684\u5e93<\/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<\/ul>\n<pre class=\"code-snippet__js\"><code>library(dplyr)<\/span><\/code><code>library(Seurat)<\/span><\/code><code>library(patchwork)<\/span><\/code><\/pre>\n<\/section>\n\u51c6\u5907\u6570\u636e<\/strong><\/span><\/p>\n\u6d4b\u8bd5\u6570\u636e\u6765\u81ea10X Genomics\u514d\u8d39\u63d0\u4f9b\u7684\u5916\u5468\u8840\u5355\u6838\u7ec6\u80de(PBMC)\u6570\u636e\u96c6\u3002\u5c06\u8fd12700\u4e2a\u7ec6\u80de\u3002\u5c0f\u679c\u5df2\u7ecf\u63d0\u524d\u8fdb\u884c\u6807\u51c6\u5316\u5904\u7406\uff0c\u5e76\u6ce8\u91ca\u597d\u4e86\u7ec6\u80de\u7c7b\u578b\uff0c\u50a8\u5b58\u4e3ards\u6587\u4ef6\u3002\u83b7\u53d6\u65b9\u5f0f\u5982\u4e0b\u3002<\/span><\/p>\n\u94fe\u63a5\uff1ahttps:\/\/pan.baidu.com\/s\/1SsrPcXyXX9qb9MtiLlIDRQ?pwd=x3mm<\/span><\/p>\n\u63d0\u53d6\u7801\uff1ax3mm<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"nginx\"><code>#\u5bfc\u5165\u6ce8\u91ca\u597d\u7684Seurat\u5bf9\u8c61<\/span><\/code><code>pbmc <- readRDS(\"pbmc3k_test.rds\")<\/span><\/code><code>#\u8fdb\u884c\u9006\u65f6\u5e8f\u5206\u6790\u9700\u8981\u51c6\u5907\u4e09\u4e2a\u6587\u4ef6\uff1a\u8868\u8fbe\u77e9\u9635\u6587\u4ef6(exprs)\u3001\u57fa\u56e0\u5c5e\u6027\u6587\u4ef6(featureData)\u548c\u7ec6#\u80de\u5c5e\u6027\u6587\u4ef6(phenoData)\uff0c\u8fd9\u4e09\u4e2a\u6587\u4ef6\u90fd\u53ef\u4ee5\u4ece\u6211\u4eec\u5904\u7406\u597d\u7684Seurat\u5bf9\u8c61\u4e2d\u83b7\u53d6\u3002<\/span><\/code><code>#\u8868\u8fbe\u77e9\u9635\uff0c\u4ee5\u7a00\u758f\u683c\u5f0f\u5904\u7406\u6570\u636e\uff0c\u53ef\u4ee5\u52a0\u5feb\u8ba1\u7b97\u901f\u5ea6<\/span><\/code><code>exprs <- as(as.matrix(pbmc@assays$RNA@counts), 'sparseMatrix')<\/span><\/code><code>#\u57fa\u56e0\u5c5e\u6027\u6587\u4ef6\uff0c\u8fd9\u662f\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u57fa\u56e0\uff0c\u6bcf\u4e00\u5217\u4ee3\u8868\u4e00\u4e2a\u5c5e\u6027\uff0c\u6bd4\u5982\u57fa\u56e0#\u540d\u3001\u57fa\u56e0\u957f\u5ea6\u7b49\u3002<\/span><\/code><code>featureData <- data.frame(gene_short_name = row.names(pbmc),row.names = row.names(pbmc))<\/span><\/code><code>fd <- new('AnnotatedDataFrame', data = featureData)<\/span><\/code><code>#\u7ec6\u80de\u5c5e\u6027\u6587\u4ef6\uff0c\u8fd9\u662f\u4e00\u4e2a\u6570\u636e\u6846\uff0c\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u7ec6\u80de\uff0c\u6bcf\u4e00\u5217\u4ee3\u8868\u4e00\u4e2a\u5c5e\u6027\uff0c\u6bd4\u5982\u7ec6\u80de#\u7c7b\u578b\u3001\u6837\u672c\u6765\u6e90\u7b49\u3002<\/span><\/code><code>phenoData <- pbmc@meta.data<\/span><\/code><code>phenoData$celltype <- pbmc@active.ident<\/span><\/code><code>pd <- new('AnnotatedDataFrame', data = phenoData)<\/span><\/code><\/pre>\n<\/section>\n\u521b\u5efa\u5bf9\u8c61<\/strong><\/span><\/p>\n#\u51c6\u5907\u597d\u4e86\u6211\u4eec\u5c31\u53ef\u4ee5\u5f00\u59cb\u7528monocle2\u7684newCellDataSet\u51fd\u6570\u6765\u521b\u5efa\u4e00\u4e2a\u5355\u7ec6\u80de\u6570\u636e\u5bf9\u8c61\uff0c#\u8fd9\u4e2a\u5bf9\u8c61\u4f1a\u5b58\u50a8\u6240\u6709\u7684\u6570\u636e\u548c\u5206\u6790\u7ed3\u679c\uff0c\u7528\u4e8e\u540e\u7eedmonocle\u5206\u6790<\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"properties\"><code>cds<\/span> <- newCellDataSet(exprs,<\/span><\/span><\/code><code>phenoData<\/span> = pd,<\/span><\/span><\/code><code>featureData<\/span> = fd,<\/span><\/span><\/code><code>lowerDetectionLimit<\/span> = 0.5,<\/span><\/span><\/code><code>expressionFamily<\/span> = negbinomial.size())<\/span><\/span><\/code><code>#\u4f30\u8ba1\u5c3a\u5bf8\u56e0\u5b50\u548c\u5206\u6563\u5ea6\uff0c\u8fd9\u4e00\u6b65\u975e\u5e38\u5173\u952e\uff0c\u4e0d\u80fd\u8df3\u8fc7<\/span><\/span><\/code><code>#\u5206\u522b\u6709\u52a9\u4e8e\u6211\u4eec\u5bf9\u8de8\u7ec6\u80de\u6355\u83b7\u7684mRNA\u5dee\u5f02\u8fdb\u884c\u5f52\u4e00\u5316\u548c\u540e\u7eed\u5dee\u5f02\u8868\u8fbe\u5206\u6790\u3002<\/span><\/span><\/code><code>cds<\/span> <- estimateSizeFactors(cds)<\/span><\/span><\/code><code>cds<\/span> <- estimateDispersions(cds)<\/span><\/span><\/code><code>##\u8fc7\u6ee4\u4f4e\u8d28\u91cf\u7ec6\u80de\uff0c\u8fc7\u6ee4\u4f4e\u4e8e1%\u7ec6\u80de\u4e2d\u68c0\u51fa\u7684\u57fa\u56e0<\/span><\/span><\/code><code>cds<\/span> <- detectGenes(cds, min_expr = 0.1)<\/span><\/span><\/code><code>#\u7b5b\u9009\u51fa\u5728\u81f3\u5c1110\u4e2a\u7ec6\u80de\u4e2d\u6709\u8868\u8fbe\u7684\u57fa\u56e0<\/span><\/span><\/code><code>#\u4ece\u5bf9\u8c61\u4e2d\u6392\u9664\u5728\u5c11\u6570\u7ec6\u80de\u4e2d\u8868\u8fbe\u7684\u57fa\u56e0\uff0c\u4ee5\u514d\u6d6a\u8d39CPU\u65f6\u95f4\u5206\u6790\u5b83\u4eec\u7684\u5dee\u5f02\u8868\u8fbe\u3002<\/span><\/span><\/code><code>expressed_genes<\/span> <- row.names(subset(fData(cds),<\/span><\/span><\/code><code>num_cells_expressed<\/span> >= 10))<\/span><\/span><\/code><\/pre>\n<\/section>\n\u7ec6\u80de\u5206\u7c7b<\/strong><\/span><\/p>\nMonocle \u63d0\u4f9b\u4e86\u4e00\u4e2a\u7b80\u5355\u7684\u7cfb\u7edf\uff0c\u7528\u4e8e\u6839\u636e\u6211\u4eec\u9009\u62e9\u7684\u6807\u8bb0\u57fa\u56e0\u7684\u8868\u8fbe\u6765\u9274\u5b9a#\u7ec6\u80de\u3002\u4f46\u662f\u672f\u4e1a\u6709\u4e13\u653b\uff0cmonocle\u6bd5\u7adf\u4e0d\u662f\u4e13\u95e8\u4f5c\u7ec6\u80de\u9274\u5b9a\u7684\u8f6f\u4ef6\uff0c\u5c0f\u679c\u8fd8\u662f\u5efa\u8bae\u5148\u505a\u597d\u7ec6#\u80de\u6ce8\u91ca\u4ee5\u540e\u518d\u5bfc\u5165monocle\u8fdb\u884c\u5206\u6790\uff0c\u8d34\u5fc3\u7684\u5c0f\u679c\u4eca\u5929\u5c31\u63d0\u524d\u5904\u7406\u4e86\uff0c\u543c\u543c~<\/span><\/p>\n\u6784\u5efa\u5355\u7ec6\u80de\u8f68\u8ff9<\/strong><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code># \u7b2c1\u6b65\uff1a\u9009\u62e9\u5b9a\u4e49\u7ec6\u80de\u8fdb\u5c55\u7684\u57fa\u56e0<\/span><\/code><code>#\u5bf9cds\u5bf9\u8c61\u4e2d\u7684expressed_genes\u57fa\u56e0\u8fdb\u884c\u5dee\u5f02\u8868\u8fbe\u5206\u6790\uff0c\u5e76\u5c06\u7ed3\u679c\u8d4b\u503c\u7ed9diff\u53d8\u91cf\u3002~ celltype\u8868\u793a\u6211\u4eec\u60f3\u8981\u6bd4\u8f83\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u4e4b\u95f4\u7684\u57fa\u56e0\u8868\u8fbe\u5dee\u5f02<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>diff <- differentialGeneTest(cds[expressed_genes,],<\/span><\/code><code>fullModelFormulaStr=\"~celltype\",<\/span><\/code><code>cores=1)<\/span><\/code><code>#\u627e\u51fa\u90a3\u4e9b\u5728\u4e0d\u540c\u7ec6\u80de\u7c7b\u578b\u4e4b\u95f4\u6709\u663e\u8457\u5dee\u5f02\u8868\u8fbe\u7684\u57fa\u56e0\uff0c\u4ee5\u7528\u4e8e\u7ec6\u80de\u6392\u5e8f\u3002<\/span><\/code><code>ordergene <- rownames(subset(diff, qval < 0.01))<\/span><\/code><code>#\u6807\u8bb0\u4e3a\u7528\u4e8e\u7ec6\u80de\u6392\u5e8f\u7684\u57fa\u56e0<\/span><\/code><code>#\u4e00\u65e6\u6211\u4eec\u6709\u4e86\u7528\u4e8e\u6392\u5e8f\u7684\u57fa\u56e0 ID \u5217\u8868\uff0c\u6211\u4eec\u9700\u8981\u5728 cds\u5bf9\u8c61\u4e2d\u8bbe\u7f6e\u5b83\u4eec\u3002<\/span><\/code><code>cds <- setOrderingFilter(cds, ordergene)<\/span><\/code><code>#\u5176\u4e2d\u9ed1\u70b9\u5c31\u662f\u540e\u9762\u6784\u5efa\u53d1\u80b2\u8f68\u8ff9\u9700\u8981\u7684\u57fa\u56e0<\/span><\/code><code>plot_ordering_genes(cds)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.869811320754717\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_caPEYfpsWD1xkxTE9mLf13uibL0ZBQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHkfDf2rLulHMeBLy6micNGFVsv0caPEYfpsWD1xkxTE9mLf13uibL0ZBQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"530\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"makefile\"><code>#\u7b2c\u4e8c\u6b65: \u964d\u4f4e\u6570\u636e\u7ef4\u5ea6<\/span><\/code><code>\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u964d\u7ef4\u5230\u4e8c\u7ef4\u7a7a\u95f4\uff0c\u6211\u4eec\u5c06\u80fd\u591f\u5728Monocle\u7ec6\u80de\u6392\u5e8f\u65f6\u8fdb\u884c\u53ef\u89c6\u5316\u548c\u89e3\u91ca\u3002<\/span><\/code><code>cds <- reduceDimension(cds, max_components = 2,<\/span><\/code><code>method = 'DDRTree')<\/span><\/code><code># \u7b2c\u4e09\u6b65: \u6cbf\u8f68\u8ff9\u5bf9\u7ec6\u80de\u8fdb\u884c\u6392\u5e8f<\/span><\/code><code>cds <- orderCells(cds)<\/span><\/code><code> <\/span><\/code><code> <\/span><\/code><code>#\u6309Pseudotime\u5c55\u793a\uff0cPseudotime\u662f\u4e00\u79cd\u7528\u6765\u8861\u91cf\u6bcf\u4e2a\u7ec6\u80de\u5728\u53d1\u80b2\u8f68\u8ff9\u4e2d\u7684\u76f8\u5bf9\u4f4d\u7f6e\u6216\u865a\u62df\u65f6\u95f4\u7684\u6307\u6807\uff0c\u5b83\u53cd\u6620\u4e86\u6bcf\u4e2a\u7ec6\u80de\u7684\u53d1\u80b2\u8fdb\u7a0b\u548c\u5206\u5316\u72b6\u6001\u3002Pseudotime\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u53d1\u73b0\u90a3\u4e9b\u968f\u7740\u53d1\u80b2\u8fc7\u7a0b\u800c\u53d8\u5316\u7684\u57fa\u56e0\u6216\u8f6c\u5f55\u56e0\u5b50\u3002<\/span><\/code><code>plot_cell_trajectory(cds,color_by=\"Pseudotime\", size=1,show_backbone=TRUE)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.869811320754717\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_fJ2oJNUyuy8HCDGB3xzSFbqyn61Fdw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHl3gDr0nfNlN9rtiaKicjEBYBpdfJ2oJNUyuy8HCDGB3xzSFbqyn61Fdw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"530\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>#\u6309\u7ec6\u80de\u7c7b\u578b\u5c55\u793a<\/span><\/code><code>plot_cell_trajectory(cds,color_by=\"celltype\", size=1,show_backbone=TRUE)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.869811320754717\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_nqIZu4naH041DvyCQUnOCic8mibnZQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHtBGnorCXqAiaGuW0NRl8f3OPApLnqIZu4naH041DvyCQUnOCic8mibnZQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"530\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code>#\u6309state\u5c55\u793a\uff0c\u8fd8\u53ef\u4ee5\u4f5c\u5206\u9762\u56fe<\/span><\/code><code>plot_cell_trajectory(cds, color_by = \"State\",size=1,show_backbone=TRUE)<\/span><\/code><code>plot_cell_trajectory(cds, color_by = \"State\") + facet_wrap(\"~State\", nrow = 1)<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.869811320754717\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_ZZV4VwJu7ewicSYqqiagkKRniaTD4A.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHOqDhhaSSPznysrlTgjV9XGDAYV1ZZV4VwJu7ewicSYqqiagkKRniaTD4A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"530\" data-recalc-dims=\"1\" \/><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.48526315789473684\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_5SZ3oeUXGHOmof4hAY69QhgaNUxfgw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHEXECvXOGB9keCnLJG1Wk7B805SZ3oeUXGHOmof4hAY69QhgaNUxfgw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"950\" data-recalc-dims=\"1\" \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code>#\u6309\u6ce8\u91ca\u4e4b\u524d\u7684\u5206\u7fa4\u7ed3\u679c\u5c55\u793a<\/span><\/code><code>plot_cell_trajectory(cds, color_by = \"seurat_clusters\")<\/span><\/code><\/pre>\n<\/section>\n<img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.869811320754717\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_V9EDbekfwrFtoQVd8aSFkWfdGrjPOg.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAxITbWibFrR6nRVnutEeqghHWsNTliaGMPrv45Pth4tTRGOmHV9EDbekfwrFtoQVd8aSFkWfdGrjPOg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"530\" data-recalc-dims=\"1\" \/><\/p>\n\u4eca\u5929\uff0c\u5c0f\u679c\u5c31\u5e26\u5927\u5bb6\u63a2\u7d22\u5230\u8fd9\u91cc\uff01\u5e0c\u671b\u4f60\u5df2\u7ecf\u7b80\u5355\u4e86\u89e3\u5982\u4f55\u4f7f\u7528Monocle2\u6765\u89c2\u5bdf\u5355\u7ec6\u80de\u7684\u53d1\u5c55\u5386\u7a0b\u3002\u5982\u679c\u6709\u4ec0\u4e48\u95ee\u9898\u6216\u8005\u7591\u95ee\uff0c\u6b22\u8fce\u5728\u8bc4\u8bba\u533a\u7559\u8a00\uff0c\u5c0f\u679c\u4f1a\u79d2\u56de\u7684\u54e6\u3002\u5982\u679c\u4f60\u89c9\u5f97\u4eca\u5929\u7684\u5185\u5bb9\u6709\u7528\uff0c\u522b\u5fd8\u4e86\u70b9\u8d5e\u548c\u5206\u4eab\u54e6\uff0c\u8fd9\u662f\u5bf9\u5c0f\u679c\u7684\u6700\u5927\u652f\u6301\uff01\u6211\u4eec\u4e0b\u6b21\u518d\u89c1\uff01<\/strong><\/span><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247493633&idx=1&sn=2263dfe7572c0bcf6816c2c1a37d79de&chksm=cf7f78c4f808f1d2209321d6ace39fde5fa60c0691b56f88eac21916f5a2872ce8ee345f1d5f&scene=21#wechat_redirect\" 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src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;\" data-recalc-dims=\"1\" \/><\/p>\n<mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<\/content>\n<\/div>\n<\/body> \n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"\u4e00\u5b66\u5c31\u4f1a\u7684\u62df\u65f6\u5e8f\u5206\u6790\uff1a\u7528Monocle2\u6d1e\u5bdf\u7ec6\u80de\u53d1\u80b2 \u539f\u521b \u5c0f\u679c 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