{"id":54125,"date":"2024-06-16T13:41:38","date_gmt":"2024-06-16T05:41:38","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54125"},"modified":"2024-06-16T13:41:38","modified_gmt":"2024-06-16T05:41:38","slug":"%e6%8e%a2%e7%b4%a2%e7%bb%86%e8%83%9e%e7%9a%84%e5%a5%87%e5%a6%99%e4%b9%8b%e6%97%85%ef%bc%9asplatter%e5%b8%a6%e4%bd%a0%e8%bd%bb%e6%9d%be%e7%8e%a9%e8%bd%ac%e5%8d%95%e7%bb%86%e8%83%9e%e6%b5%8b%e5%ba%8f","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=54125","title":{"rendered":"\u63a2\u7d22\u7ec6\u80de\u7684\u5947\u5999\u4e4b\u65c5\uff1asplatter\u5e26\u4f60\u8f7b\u677e\u73a9\u8f6c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\uff01\uff08\u4e8c\uff09"},"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 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 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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=3138222091851530242#wechat_redirect\" title=\"\u751f\u4fe1\u6709\u5173\u7edf\u8ba1\" target=\"_blank\" rel=\"noopener\">#\u751f\u4fe1\u6709\u5173\u7edf\u8ba1<\/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<section data-mpa-powered-by=\"yiban.io\">\n<section powered-by=\"xiumi.us\">\n<section>\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section powered-by=\"xiumi.us\">\n<section>\n<section>\n<section powered-by=\"xiumi.us\">\n<section powered-by=\"xiumi.us\">\n<section>\n<p><span style=\"text-indent: 0em;color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u5728\u4e0a\u4e00\u7bc7\u6559\u7a0b\u4e2d\uff0c\u5c0f\u679c\u6559\u5927\u5bb6\u5982\u4f55\u4f7f\u7528<\/span><span style=\"text-indent: 0em;color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">splatter<\/span><span style=\"text-indent: 0em;color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u548c<\/span><span style=\"text-indent: 0em;color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">scater<\/span><span style=\"text-indent: 0em;color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u5305\u8fdb\u884c\u5355\u7ec6\u80de\u6d4b\u5e8f\u6570\u636e\u7684\u6a21\u62df\u548c\u5206\u6790\uff0c\u5176\u4e2d\u5305\u62ec\u6a21\u62df\u6570\u636e\u7684\u5feb\u901f\u751f\u6210\u3001\u53c2\u6570\u4f30\u8ba1\u3001\u81ea\u5b9a\u4e49\u53c2\u6570\u521b\u5efa\u3001\u6570\u636e\u63d0\u53d6\u3001\u6570\u636e\u6807\u51c6\u5316\u548c\u964d\u7ef4\u5904\u7406\u7b49\uff0c\u90a3\u4e48\u4eca\u5929\u5c0f\u679c\u6765\u7ee7\u7eed\u5e26\u5927\u5bb6\u5b66\u4e60\u8fd9\u4e2a<\/span><span style=\"text-indent: 0em;color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">R<\/span><span style=\"text-indent: 0em;color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u5305\u7684\u4f7f\u7528\u65b9\u6cd5\uff0c\u4eca\u5929\u7684\u5b66\u4e60\u4e5f\u5c06\u57fa\u4e8e\u6628\u5929\u7684\u4ee3\u7801\u54e6\uff0c\u60f3\u8981\u6df1\u5165\u5b66\u4e60\u7684\u5c0f\u4f19\u4f34\u548c\u5c0f\u679c\u4e00\u8d77\u770b\u4e0b\u53bb\u5427\uff01<\/span><span style=\"font-size: var(--articleFontsize);letter-spacing: 0.034em;text-align: center;text-indent: 0em;\"><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"color: rgb(255, 129, 36);font-size: 12px;letter-spacing: 0.5px;\"><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"color: rgb(51, 51, 51);font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 14px;color: rgb(51, 51, 51);\">\u9996\u5148\uff0c\u6211\u4eec\u6765\u56de\u987e\u4e00\u4e0b\u4e0a\u4e00\u7bc7\u4e2d\u4f7f\u7528<\/span>splatter<span style=\"font-size: 14px;color: rgb(51, 51, 51);\">\u5305\u7684\u4ee3\u7801\uff1a<\/span><\/span><\/p>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\n<h1 style=\"text-align: center;\"><em style=\"letter-spacing: 0.034em;\"><\/em><\/h1>\n<\/section>\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\">\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<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<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=\"makefile\"><code><span class=\"code-snippet_outer\">library(splatter)<\/span><\/code><code><span class=\"code-snippet_outer\">library(scater)<\/span><\/code><code><span class=\"code-snippet_outer\">set.seed(1)<\/span><\/code><code><span class=\"code-snippet_outer\">sce <- mockSCE() <span class=\"code-snippet__comment\"># class: SingleCellExperiment<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">counts(sce)<\/span><\/code><code><span class=\"code-snippet_outer\">params <- splatEstimate(sce) <span class=\"code-snippet__comment\"># Params object<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">params <- newSplatParams() <span class=\"code-snippet__comment\">#\u9ed8\u8ba410000 Genes\uff0c100 Cells<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">getParam(params, <span class=\"code-snippet__string\">\"nGenes\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">getParam(params, <span class=\"code-snippet__string\">\"nCells\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">getParams(params, c(<span class=\"code-snippet__string\">\"nGenes\"<\/span>, <span class=\"code-snippet__string\">\"mean.rate\"<\/span>, <span class=\"code-snippet__string\">\"mean.shape\"<\/span>))<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParam(params, <span class=\"code-snippet__string\">\"nGenes\"<\/span>, 5000)<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParam(params, <span class=\"code-snippet__string\">\"batchCells\"<\/span>, 50)<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParams(params, mean.shape = 0.5, de.prob = 0.2)<\/span><\/code><code><span class=\"code-snippet_outer\">params <- setParams(params, update = list(nGenes = 8000, mean.rate = 0.5))<\/span><\/code><code><span class=\"code-snippet_outer\">sim <- splatSimulate(params)<\/span><\/code><code><span class=\"code-snippet_outer\">class(sim)<\/span><\/code><code><span class=\"code-snippet_outer\">head(rowData(sim))<\/span><\/code><code><span class=\"code-snippet_outer\">head(colData(sim))<\/span><\/code><code><span class=\"code-snippet_outer\">names(assays(sim))<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__section\">assays(sim)$CellMeans[1:5, 1:5]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">counts <- counts(sim)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__section\">counts[1:3,1:5]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">class(counts) <span class=\"code-snippet__comment\"># \"matrix\" \"array\" <\/span><\/span><\/code><code><span class=\"code-snippet_outer\">typeof(counts) <span class=\"code-snippet__comment\"># [1] \"integer\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">dim(counts) <span class=\"code-snippet__comment\">#[1] 8000 100<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim <- logNormCounts(sim)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__section\">counts(sim)[1:3,1:5]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__section\">logcounts(sim)[1:3,1:5]<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim <- runPCA(sim)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.groups <- splatSimulate(group.prob = c(0.3, 0.7), method = <span class=\"code-snippet__string\">\"groups\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">                           verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.groups <- logNormCounts(sim.groups)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.groups <- runPCA(sim.groups)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim.groups, colour_by = <span class=\"code-snippet__string\">\"Group\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">dim(counts(sim.groups))<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.groups)$DEFacGroup1<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.groups)$DEFacGroup2<\/span><\/code><code><span class=\"code-snippet_outer\">metadata(sim.groups)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.paths <- splatSimulate(de.prob = 0.2, nGenes = 1000, method = <span class=\"code-snippet__string\">\"paths\"<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">                           verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.paths <- logNormCounts(sim.paths)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.paths <- runPCA(sim.paths)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim.paths, colour_by = <span class=\"code-snippet__string\">\"Step\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">colData(sim.paths)$Step<\/span><\/code><code><span class=\"code-snippet_outer\">sim.batches <- splatSimulate(batchCells = c(50, 50), verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.batches <- logNormCounts(sim.batches)<\/span><\/code><code><span class=\"code-snippet_outer\">sim.batches <- runPCA(sim.batches)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim.batches, colour_by = <span class=\"code-snippet__string\">\"Batch\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.batches)$BatchFacBatch1<\/span><\/code><code><span class=\"code-snippet_outer\">rowData(sim.batches)$BatchFacBatch2<\/span><\/code><code><span class=\"code-snippet_outer\">dev.off()<\/span><\/code><\/pre>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\">\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.3888888888888889\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_IlmBAWe69EMUPMhNEgrv6NXX85lJxg-14.jpg?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwyrj7kbUR3ULG9ZUbLrLkgibzL8qUpQROfe8ebc3gNSnu1dIlmBAWe69EMUPMhNEgrv6NXX85lJxg\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"color: rgb(51, 51, 51);\">\u7ee7\u7eed\u4e0a\u9762\u7684\u64cd\u4f5c\uff0c\u6211\u4eec\u6765\u7ee7\u7eed\u5b66\u4e60\u8fd9\u4e2a\u5305\u7684\u5e94\u7528\uff1a<\/span><\/span><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">\u6bd4\u8f83SingleCellExperiment\u5bf9\u8c61<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u9996\u5148\u6211\u4eec\u4f7f\u7528splatSimulate\u51fd\u6570\u751f\u6210\u4e24\u4e2aSingleCellExperiment\u5bf9\u8c61sim1\u548csim2\uff0c\u5206\u522b\u8868\u793a\u4e24\u4e2a\u4e0d\u540c\u7684\u5b9e\u9a8c\u6761\u4ef6\u3002<\/span><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\">\u7136\u540e\u4f7f\u7528compareSCEs\u51fd\u6570\u5c06\u8fd9\u4e24\u4e2a\u5bf9\u8c61\u8fdb\u884c\u6bd4\u8f83\uff0c\u5e76\u5c06\u7ed3\u679c\u4fdd\u5b58\u5728comparison\u53d8\u91cf\u4e2d\u3002<\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Open Sans';mso-fareast-font-family:\u5b8b\u4f53;color:rgb(51,51,51);font-size:12.0000pt;mso-font-kerning:0.0000pt;\"><o:p><\/o:p><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">### 7.\u6bd4\u8f83SingleCellExperiment\u5bf9\u8c61<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u76f8\u4e92\u6bd4\u8f83<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- splatSimulate(nGenes = <span class=\"code-snippet__number\">1000<\/span>, batchCells = <span class=\"code-snippet__number\">20<\/span>, verbose = <span class=\"code-snippet__keyword\">FALSE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- simpleSimulate(nGenes = <span class=\"code-snippet__number\">1000<\/span>, nCells = <span class=\"code-snippet__number\">20<\/span>, verbose = <span class=\"code-snippet__keyword\">FALSE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">comparison <- compareSCEs(<span class=\"code-snippet__keyword\">list<\/span>(Splat = sim1, Simple = sim2))<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u63a5\u7740\uff0c\u6211\u4eec\u6765\u5b66\u4e60\u5982\u4f55\u8bbf\u95eecomparison\u5bf9\u8c61\u4e2d\u7684\u4e0d\u540c\u5c5e\u6027\uff0c\u5305\u62ecRowData\u548cColData\uff0c\u4ee5\u53caPlots\u4e2d\u7684Means\u3001LibrarySizes\u548cZerosCell\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"bash\"><code><span class=\"code-snippet_outer\">names(comparison)<\/span><\/code><code><span class=\"code-snippet_outer\">comparison<span class=\"code-snippet__variable\">$RowData<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">comparison<span class=\"code-snippet__variable\">$ColData<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">names(comparison<span class=\"code-snippet__variable\">$Plots<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">comparison<span class=\"code-snippet__variable\">$Plots<\/span><span class=\"code-snippet__variable\">$Means<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">comparison<span class=\"code-snippet__variable\">$Plots<\/span><span class=\"code-snippet__variable\">$LibrarySizes<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">comparison<span class=\"code-snippet__variable\">$Plots<\/span><span class=\"code-snippet__variable\">$ZerosCell<\/span><\/span><\/code><\/pre>\n<\/section>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.6435786435786436\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ARhibYbnNz5iaCqrLBHmE8Dg0ZcwIA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAy6nCYibdkPuFzMl1gf54TicBYO0eu8icALztibXwdvDMsHFoQj86ARhibYbnNz5iaCqrLBHmE8Dg0ZcwIA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1.331002331002331\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_aLIMTV6QyaiaR77c6lW5sNjCeXhyaw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAy6nCYibdkPuFzMl1gf54TicBEHn9e44XHxkxr1anCU8HIcHOciaLIMTV6QyaiaR77c6lW5sNjCeXhyaw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"429\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p><span style=\"color: rgb(51, 51, 51);font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"color: rgb(51, 51, 51);\">\u4e4b\u540e\uff0c\u4ee3\u7801\u518d\u6b21\u751f\u6210\u4e09\u4e2a<\/span>SingleCellExperiment<span style=\"color: rgb(51, 51, 51);\">\u5bf9\u8c61\uff0c\u5206\u522b\u547d\u540d\u4e3a<\/span>sim1<span style=\"color: rgb(51, 51, 51);\">\u3001<\/span>sim2<span style=\"color: rgb(51, 51, 51);\">\u548c<\/span>sim3<span style=\"color: rgb(51, 51, 51);\">\u3002\u7136\u540e\u4f7f\u7528<\/span>diffSCEs<span style=\"color: rgb(51, 51, 51);\">\u51fd\u6570\u5c06\u8fd9\u4e09\u4e2a\u5bf9\u8c61\u4e0e\u53c2\u8003\u5bf9\u8c61<\/span>“Simple”<span style=\"color: rgb(51, 51, 51);\">\u8fdb\u884c\u6bd4\u8f83\uff0c\u5e76\u5c06\u7ed3\u679c\u4fdd\u5b58\u5728<\/span>difference<span style=\"color: rgb(51, 51, 51);\">\u53d8\u91cf\u4e2d\u3002<\/span><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"php\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\">## \u4e0e\u53c2\u8003\u8fdb\u884c\u6bd4\u8f83<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- splatSimulate(nGenes = <span class=\"code-snippet__number\">1000<\/span>, batchCells = <span class=\"code-snippet__number\">100<\/span>, verbose = <span class=\"code-snippet__keyword\">FALSE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- splatSimulate(nGenes = <span class=\"code-snippet__number\">1000<\/span>, batchCells = c(<span class=\"code-snippet__number\">40<\/span>, <span class=\"code-snippet__number\">60<\/span>), verbose = <span class=\"code-snippet__keyword\">FALSE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">sim3 <- simpleSimulate(nGenes = <span class=\"code-snippet__number\">1000<\/span>, nCells = <span class=\"code-snippet__number\">100<\/span>, verbose = <span class=\"code-snippet__keyword\">FALSE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">difference <- diffSCEs(<span class=\"code-snippet__keyword\">list<\/span>(Splat1 = sim1, Splat2 = sim2, Simple = sim3), ref = <span class=\"code-snippet__string\">\"Simple\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">difference$Plots$Means<\/span><\/code><code><span class=\"code-snippet_outer\">difference$QQPlots$Means<\/span><\/code><\/pre>\n<\/section>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">\u6279\u6b21\u6548\u5e94\u53c2\u6570\u8bbe\u7f6e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-align: justify;\"><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;text-align: justify;\">\u63a5\u4e0b\u6765\uff0c\u6211\u4eec\u5b66\u4e60\u5982\u4f55\u4f7f\u7528splatSimulate\u51fd\u6570\u751f\u6210\u5e26\u6709\u6279\u6b21\u6548\u5e94\u7684\u6570\u636e\u3002<\/span><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;text-align: justify;\">\u4ee5\u4e0b\u4ee3\u7801\u5206\u522b\u751f\u6210\u4e86\u4e24\u4e2aSingleCellExperiment\u5bf9\u8c61sim1\u548csim2\uff0c\u4f7f\u7528\u4e0d\u540c\u7684\u6279\u6b21\u6548\u5e94\u53c2\u6570\u3002<\/span><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;text-align: justify;\">\u7136\u540e\u5bf9\u8fd9\u4e24\u4e2a\u5bf9\u8c61\u8fdb\u884c\u4e86log2\u6807\u51c6\u5316\u548cPCA\u5206\u6790\uff0c\u5e76\u4f7f\u7528plotPCA\u51fd\u6570\u5c06\u7ed3\u679c\u53ef\u89c6\u5316\u3002<\/span><br \/><\/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<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"splatter\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"scater\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">library(<span class=\"code-snippet__string\">\"ggplot2\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># Simulation with small batch effects<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- splatSimulate(<span class=\"code-snippet__keyword\">params<\/span>, batchCells = c(<span class=\"code-snippet__number\">100<\/span>, <span class=\"code-snippet__number\">100<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">                     batch.facLoc = <span class=\"code-snippet__number\">0.001<\/span>, batch.facScale = <span class=\"code-snippet__number\">0.001<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">                     verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- logNormCounts(sim1)<\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- runPCA(sim1)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim1, colour_by = <span class=\"code-snippet__string\">\"Batch\"<\/span>) + ggtitle(<span class=\"code-snippet__string\">\"Small batch effects\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># Simulation with big batch effects<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- splatSimulate(<span class=\"code-snippet__keyword\">params<\/span>, batchCells = c(<span class=\"code-snippet__number\">100<\/span>, <span class=\"code-snippet__number\">100<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">                     batch.facLoc = <span class=\"code-snippet__number\">0.5<\/span>, batch.facScale = <span class=\"code-snippet__number\">0.5<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">                     verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- logNormCounts(sim2)<\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- runPCA(sim2)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim2, colour_by = <span class=\"code-snippet__string\">\"Batch\"<\/span>) + ggtitle(<span class=\"code-snippet__string\">\"Big batch effects\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"color: rgb(51, 51, 51);font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u6211\u4eec\u5206\u522b\u6765\u770b\u4e0b\u4e24\u6b21\u53ef\u89c6\u5316\u540e\u7684\u7ed3\u679c\u5427\uff01<\/span><\/p>\n<p><span style=\"mso-spacerun:'yes';font-family:'Open Sans';mso-fareast-font-family:\u5b8b\u4f53;color:rgb(51,51,51);font-size:12.0000pt;mso-font-kerning:0.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_bOM1Jeaf8h8MADEzbiaWWs4coTpk5w.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAy6nCYibdkPuFzMl1gf54TicBTiaYHc9byyViaZFBdNcAHV5BOJDibOM1Jeaf8h8MADEzbiaWWs4coTpk5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_P8p1ksVAbMUrpEaNO98Yt1GFVPx4Uw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAy6nCYibdkPuFzMl1gf54TicBFBC4k1U0fybGGMb35nQRLn3pP8p1ksVAbMUrpEaNO98Yt1GFVPx4Uw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u63a5\u7740\uff0c\u5c0f\u679c\u5411\u5927\u5bb6\u5c55\u793a\u4e86\u5982\u4f55\u8bbe\u7f6e\u6279\u6b21\u6548\u5e94\u53c2\u6570\u6765\u6d88\u9664\u6279\u6b21\u6548\u5e94\u3002\u9996\u5148\u751f\u6210\u4e00\u4e2a\u5e26\u6709\u6279\u6b21\u6548\u5e94\u7684\u6570\u636esim1\uff0c\u7136\u540e\u4e0d\u79fb\u9664\u6279\u6b21\u6548\u5e94\u8fdb\u884clog2\u6807\u51c6\u5316\u548cPCA\u5206\u6790\uff1b\u63a5\u7740\u751f\u6210\u4e00\u4e2a\u6ca1\u6709\u6279\u6b21\u6548\u5e94\u7684\u6570\u636esim2\uff0c\u7136\u540e\u5bf9\u5176\u8fdb\u884clog2\u6807\u51c6\u5316\u548cPCA\u5206\u6790\u3002\u6700\u540e\uff0c\u4f7f\u7528plotPCA\u51fd\u6570\u5c06\u7ed3\u679c\u53ef\u89c6\u5316\u5e76\u8fdb\u884c\u5bf9\u6bd4\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"objectivec\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># \u662f\u5426\u6d88\u9664\u6279\u6b21\u6548\u5e94\u8bbe\u7f6e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- splatSimulate(params, batchCells = c(<span class=\"code-snippet__number\">100<\/span>, <span class=\"code-snippet__number\">100<\/span>), batch.rmEffect = <span class=\"code-snippet__literal\">FALSE<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">                     verbose = <span class=\"code-snippet__literal\">FALSE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- logNormCounts(sim1)<\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- runPCA(sim1)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim1, colour_by = <span class=\"code-snippet__string\">\"Batch\"<\/span>) + ggtitle(<span class=\"code-snippet__string\">\"With batch effects\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- splatSimulate(params, batchCells = c(<span class=\"code-snippet__number\">100<\/span>, <span class=\"code-snippet__number\">100<\/span>), batch.rmEffect = <span class=\"code-snippet__literal\">TRUE<\/span>,<\/span><\/code><code><span class=\"code-snippet_outer\">                     verbose = <span class=\"code-snippet__literal\">FALSE<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- logNormCounts(sim2)<\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- runPCA(sim2)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim2, colour_by = <span class=\"code-snippet__string\">\"Batch\"<\/span>) + ggtitle(<span class=\"code-snippet__string\">\"Batch effects removed\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"color: rgb(51, 51, 51);font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u53ef\u89c6\u5316\u540e\u7684\u7ed3\u679c\u5982\u4e0b\uff1a<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.9913419913419913\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_F4r1LooROaxm0bjuexeCrrX5I4STtA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAy6nCYibdkPuFzMl1gf54TicBFrVbTic9TljNHLs4LT6FBib5BNF4r1LooROaxm0bjuexeCrrX5I4STtA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">\u79bb\u7fa4\u503c\u53c2\u6570\u8bbe\u7f6e<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-align: justify;\"><span style=\"text-align: justify;font-size: 14px;letter-spacing: 0.034em;\">\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u5c06\u5c55\u793a\u4e86\u5982\u4f55\u8bbe\u7f6e\u79bb\u7fa4\u503c\u53c2\u6570\uff0c\u5e76\u4f7f\u7528splatSimulate\u51fd\u6570\u751f\u6210\u5e26\u6709\u79bb\u7fa4\u503c\u7684\u6570\u636e\u3002<\/span><span style=\"text-align: justify;font-size: 14px;letter-spacing: 0.034em;\">\u4ee5\u4e0b\u4ee3\u7801\u5206\u522b\u751f\u6210\u4e86\u4e24\u4e2aSingleCellExperiment\u5bf9\u8c61sim1\u548csim2\uff0c\u4f7f\u7528\u4e0d\u540c\u7684\u79bb\u7fa4\u503c\u6982\u7387\u53c2\u6570\u3002<\/span><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;\"><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">### 9. \u79bb\u7fa4\u503c\u53c2\u6570\u8bbe\u7f6e<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">## ----outlier-prob-------------------------------------------------------------<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># Few outliers<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- splatSimulate(<span class=\"code-snippet__keyword\">out<\/span>.prob = <span class=\"code-snippet__number\">0.001<\/span>, verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(<span class=\"code-snippet__keyword\">as<\/span>.data.frame(rowData(sim1)),<\/span><\/code><code><span class=\"code-snippet_outer\">       aes(x = log10(GeneMean), fill = OutlierFactor != <span class=\"code-snippet__number\">1<\/span>)) +<\/span><\/code><code><span class=\"code-snippet_outer\"> geom_histogram(bins = <span class=\"code-snippet__number\">100<\/span>) +<\/span><\/code><code><span class=\"code-snippet_outer\"> ggtitle(<span class=\"code-snippet__string\">\"Few outliers\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># Lots of outliers<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- splatSimulate(<span class=\"code-snippet__keyword\">out<\/span>.prob = <span class=\"code-snippet__number\">0.2<\/span>, verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">ggplot(<span class=\"code-snippet__keyword\">as<\/span>.data.frame(rowData(sim2)),<\/span><\/code><code><span class=\"code-snippet_outer\">       aes(x = log10(GeneMean), fill = OutlierFactor != <span class=\"code-snippet__number\">1<\/span>)) +<\/span><\/code><code><span class=\"code-snippet_outer\"> geom_histogram(bins = <span class=\"code-snippet__number\">100<\/span>) +<\/span><\/code><code><span class=\"code-snippet_outer\"> ggtitle(<span class=\"code-snippet__string\">\"Lots of outliers\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\">\u6700\u540e\u7ed8\u56fe\u7ed3\u679c\u8ba9\u6211\u4eec\u6765\u4e00\u8d77\u770b\u4e00\u4e0b\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:'Open Sans';mso-fareast-font-family:\u5b8b\u4f53;color:rgb(51,51,51);font-size:12.0000pt;mso-font-kerning:0.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p><span style=\"font-size: 14px;\"><span style=\"font-family: "Open Sans";color: rgb(51, 51, 51);font-size: 12pt;\"><o:p><\/o:p><\/span><\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.9971139971139971\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_7jCD5omVrXZic0xYia5zzC40ibo1eQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAy6nCYibdkPuFzMl1gf54TicBnTIPLFWGwxZuX5L9zGzmVnZfoib67jCD5omVrXZic0xYia5zzC40ibo1eQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section data-mpa-template=\"t\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 16px;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row;margin-top: 10px;margin-bottom: 10px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;align-self: flex-end;flex: 0 0 auto;border-style: solid;border-width: 0px 0px 7px;border-bottom-color: rgb(175, 225, 255);min-width: 5%;height: auto;\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;font-size: 20px;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><strong mpa-from-tpl=\"t\" mpa-is-content=\"t\">\u8bbe\u7f6e\u7ec4\u53c2\u6570<\/strong><\/p>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;vertical-align: bottom;width: auto;min-width: 5%;flex: 0 0 auto;height: auto;align-self: flex-end;\" mpa-from-tpl=\"t\">\n<section style=\"transform: perspective(0px);transform-style: flat;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<section style=\"transform: translate3d(5px, 0px, 0px) rotateX(180deg);\" mpa-from-tpl=\"t\">\n<section style=\"display: inline-block;width: 6px;height: 6px;vertical-align: top;overflow: hidden;border-radius: 460px;background-color: rgb(244, 171, 189);\" mpa-from-tpl=\"t\">\n<section style=\"text-align: justify;\" powered-by=\"xiumi.us\" mpa-from-tpl=\"t\">\n<p><br mpa-from-tpl=\"t\" \/><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-align: justify;\"><span style=\"text-align: justify;font-size: 14px;letter-spacing: 0.034em;\">\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u5c06\u6559\u5927\u5bb6\u5982\u4f55\u8bbe\u7f6e\u7ec4\u53c2\u6570\uff0c\u5e76\u4f7f\u7528splatSimulateGroups\u51fd\u6570\u751f\u6210\u5177\u6709\u4e0d\u540c\u7ec4\u7684\u6570\u636e\u3002<\/span><span style=\"text-align: justify;font-size: 14px;letter-spacing: 0.034em;\">\u9996\u5148\u6211\u4eec\u6076\u610f\u751f\u6210\u4e00\u4e2a\u5305\u542b\u4e00\u4e2a\u5c0f\u7ec4\u548c\u4e00\u4e2a\u5927\u7ec4\u7684\u6570\u636esim1\uff0c\u7136\u540e\u5bf9\u5176\u8fdb\u884clog2\u6807\u51c6\u5316\u548cPCA\u5206\u6790\uff1b<\/span><span style=\"text-align: justify;font-size: 14px;letter-spacing: 0.034em;\">\u63a5\u7740\u751f\u6210\u4e00\u4e2a\u5305\u542b\u4e94\u4e2a\u7ec4\u7684\u6570\u636esim2\uff0c\u7136\u540e\u5bf9\u5176\u8fdb\u884clog2\u6807\u51c6\u5316\u548cPCA\u5206\u6790\u3002<\/span><span style=\"text-align: justify;font-size: 14px;letter-spacing: 0.034em;\">\u6700\u540e\uff0c\u4f7f\u7528plotPCA\u51fd\u6570\u5c06\u7ed3\u679c\u53ef\u89c6\u5316\u5e76\u8fdb\u884c\u5bf9\u6bd4\u3002<\/span><br \/><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">### 10.\u8bbe\u7f6e\u7ec4\u53c2\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># One small group, one big group<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">params<\/span>.groups <- newSplatParams(batchCells = <span class=\"code-snippet__number\">500<\/span>, nGenes = <span class=\"code-snippet__number\">1000<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- splatSimulateGroups(<span class=\"code-snippet__keyword\">params<\/span>.groups, <span class=\"code-snippet__keyword\">group<\/span>.prob = c(<span class=\"code-snippet__number\">0.9<\/span>, <span class=\"code-snippet__number\">0.1<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">                           verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- logNormCounts(sim1)<\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- runPCA(sim1)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim1, colour_by = <span class=\"code-snippet__string\">\"Group\"<\/span>) + ggtitle(<span class=\"code-snippet__string\">\"One small group, one big group\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># Five groups<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- splatSimulateGroups(<span class=\"code-snippet__keyword\">params<\/span>.groups,<\/span><\/code><code><span class=\"code-snippet_outer\">                           <span class=\"code-snippet__keyword\">group<\/span>.prob = c(<span class=\"code-snippet__number\">0.2<\/span>, <span class=\"code-snippet__number\">0.2<\/span>, <span class=\"code-snippet__number\">0.2<\/span>, <span class=\"code-snippet__number\">0.2<\/span>, <span class=\"code-snippet__number\">0.2<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">                           verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- logNormCounts(sim2)<\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- runPCA(sim2)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim2, colour_by = <span class=\"code-snippet__string\">\"Group\"<\/span>) + ggtitle(<span class=\"code-snippet__string\">\"Five groups\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"color: rgb(51, 51, 51);font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u53ef\u89c6\u5316\u540e\u7684\u7ed3\u679c\u5982\u4e0b\uff1a<\/span><span style=\"mso-spacerun:'yes';font-family:'Open Sans';mso-fareast-font-family:\u5b8b\u4f53;color:rgb(51,51,51);font-size:12.0000pt;mso-font-kerning:0.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><em><strong><span style=\"font-size: 20px;\"><\/span><\/strong><\/em><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.9971139971139971\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/8_aibP9mW83BVmn4VCWiblAUNXwSerzw.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAy6nCYibdkPuFzMl1gf54TicBXzakVbjRiaDicROb81sQTh883Tz4iaibP9mW83BVmn4VCWiblAUNXwSerzw\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\" \/><\/p>\n<p><span style=\"color: rgb(51, 51, 51);font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 14px;color: rgb(51, 51, 51);\">\u6700\u540e\uff0c\u5c0f\u679c\u5c06\u5c55\u793a\u4e86\u5982\u4f55\u8bbe\u7f6e\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u53c2\u6570\uff0c\u5e76\u4f7f\u7528<\/span>splatSimulateGroups<span style=\"font-size: 14px;color: rgb(51, 51, 51);\">\u51fd\u6570\u751f\u6210\u5177\u6709\u4e0d\u540c\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u7684\u6570\u636e\u3002<\/span><\/span><span style=\"mso-spacerun:'yes';font-family:'Open Sans';mso-fareast-font-family:\u5b8b\u4f53;color:rgb(51,51,51);font-size:12.0000pt;mso-font-kerning:0.0000pt;\"><o:p><\/o:p><\/span><\/p>\n<p style=\"text-align: center;\"><em><strong><span style=\"font-size: 20px;\"><\/span><\/strong><\/em><\/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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"cs\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">### 11. \u8bbe\u7f6e\u5dee\u5f02\u8868\u8fbe\u57fa\u56e0\u53c2\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">## de.prob \u53c2\u6570<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># Few DE genes<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">params<\/span>.groups <- newSplatParams(batchCells = <span class=\"code-snippet__number\">500<\/span>, nGenes = <span class=\"code-snippet__number\">1000<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- splatSimulateGroups(<span class=\"code-snippet__keyword\">params<\/span>.groups, <span class=\"code-snippet__keyword\">group<\/span>.prob = c(<span class=\"code-snippet__number\">0.5<\/span>, <span class=\"code-snippet__number\">0.5<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">                           de.prob = <span class=\"code-snippet__number\">0.01<\/span>, verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- logNormCounts(sim1)<\/span><\/code><code><span class=\"code-snippet_outer\">sim1 <- runPCA(sim1)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim1, colour_by = <span class=\"code-snippet__string\">\"Group\"<\/span>) + ggtitle(<span class=\"code-snippet__string\">\"Few DE genes\"<\/span>)<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\"># Lots of DE genes<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- splatSimulateGroups(<span class=\"code-snippet__keyword\">params<\/span>.groups, <span class=\"code-snippet__keyword\">group<\/span>.prob = c(<span class=\"code-snippet__number\">0.5<\/span>, <span class=\"code-snippet__number\">0.5<\/span>),<\/span><\/code><code><span class=\"code-snippet_outer\">                           de.prob = <span class=\"code-snippet__number\">0.3<\/span>, verbose = FALSE)<\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- logNormCounts(sim2)<\/span><\/code><code><span class=\"code-snippet_outer\">sim2 <- runPCA(sim2)<\/span><\/code><code><span class=\"code-snippet_outer\">plotPCA(sim2, colour_by = <span class=\"code-snippet__string\">\"Group\"<\/span>) + ggtitle(<span class=\"code-snippet__string\">\"Lots of DE genes\"<\/span>)<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"color: rgb(51, 51, 51);font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\">\u53ef\u89c6\u5316\u540e\u7684\u7ed3\u679c\u5982\u4e0b\uff1a<\/span><\/p>\n<p style=\"text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"1.0101010101010102\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/9_gd31n1yevFyGbCC6g5Gxe3JYZv2ELQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAy6nCYibdkPuFzMl1gf54TicBQTic9bbgyhzGTF6Z0YUOXGU7xgd31n1yevFyGbCC6g5Gxe3JYZv2ELQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"693\" style=\"\" data-recalc-dims=\"1\"><span style=\"color: rgb(51, 51, 51);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.034em;text-align: justify;\"><\/span><\/p>\n<p style=\"text-align: center;\"><em><strong><span style=\"font-size: 20px;\"><\/span><\/strong><\/em><\/p>\n<p style=\"text-align: left;\"><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 14px;color: rgb(51, 51, 51);\"><span style=\"font-size: 14px;\">\u5982\u4f55\uff0c\u8fd9\u51e0\u4e2a<\/span>splatter<span style=\"font-size: 14px;\">\u7684\u76f8\u5173\u5e94\u7528\u4f60\u5b66\u4f1a\u4e86\u561b\uff1f\u662f\u4e0d\u662f\u5f88\u7b80\u5355\uff01\u66f4\u591a\u5b66\u4e60\u5e72\u8d27\u8981\u591a\u591a\u5173\u6ce8<\/span><\/span><span style=\"font-size: 14px;color: rgb(51, 51, 51);\">\u5c0f<\/span><span style=\"font-size: 14px;color: rgb(51, 51, 51);\">\u679c\u54e6\uff01<\/span><\/span><strong style=\"letter-spacing: 0.578px;font-size: var(--articleFontsize);text-align: justify;\"><span style=\"letter-spacing: 0.578px;text-align: left;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;\"><\/span><\/strong><span style=\"font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;font-size: 14px;letter-spacing: 0.578px;\"><\/span><strong style=\"color: rgb(121, 123, 170);font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;outline: 0px;font-size: 15px;letter-spacing: 0.544px;background-color: rgb(255, 255, 255);\"><\/strong><\/p>\n<section powered-by=\"xiumi.us\" style=\"margin-bottom: 0px;letter-spacing: 0.578px;white-space: normal;text-align: left;\">\n<section style=\"font-size: 16px;\">\n<section powered-by=\"xiumi.us\" style=\"margin: 10px;justify-content: flex-start;display: flex;flex-flow: row;\">\n<section style=\"padding-right: 10px;padding-left: 10px;display: inline-block;width: 558px;vertical-align: top;border-style: dashed;border-width: 1px;border-color: rgb(62, 62, 62);align-self: flex-start;flex: 0 0 auto;\">\n<section powered-by=\"xiumi.us\" style=\"margin-top: 10px;margin-bottom: 10px;\">\n<section style=\"display: inline-block;width: 536px;border-width: 0px 0px 0px 10px;border-style: solid;border-left-color: rgb(144, 215, 236);border-right-color: rgb(46, 172, 109);box-shadow: rgb(0, 0, 0) 0px 0px 0px;border-bottom-left-radius: 0px;\">\n<section powered-by=\"xiumi.us\" style=\"padding-right: 3px;padding-left: 3px;\">\n<section style=\"margin-top: 0.95em;margin-bottom: -0.65em;display: inline-block;width: 520px;vertical-align: top;\">\n<section style=\"width: 520px;\">\n<section style=\"border-top: 1px solid rgb(0, 0, 0);width: 519.479px;float: left;\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<section style=\"margin-top: -3px;width: 6px;height: 6px;border-radius: 100%;float: right;background-color: rgb(46, 172, 109);\"><svg viewbox=\"0 0 1 1\" style=\"float:left;line-height:0;width:0;vertical-align:top;\"><\/svg><\/section>\n<\/section>\n<section style=\"margin-top: -1em;padding: 3px 10px;display: inline-block;vertical-align: top;background-color: rgb(255, 255, 255);color: rgb(0, 154, 68);\">\n<p><strong>\u5f80\u671f\u63a8\u8350<\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section powered-by=\"xiumi.us\" style=\"text-align: justify;\">\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491794&idx=1&sn=2b7a4de95169c79202e44813885a8250&chksm=cf7f7017f808f9015689839fe4057fd418bf7b20eb1dfb5a28cd92e56a41b5605e62bfbc16fb&scene=21#wechat_redirect\" textvalue=\"1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\"><span style=\"font-size: 14px;\">1.\u642d\u5efa\u751f\u4fe1\u5206\u6790\u6d41\u6c34\u7ebf\uff0c\u5982\u5de5\u5382\u4e00\u683724\u5c0f\u65f6\u8fd0\u8f6cSnakemake\u2014\u2014\u8fdb\u9636\u547d\u4ee4<\/span><\/a><br \/><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491705&idx=1&sn=9ff9b6da28b3a256a99c6697d589be66&chksm=cf7f70bcf808f9aafd1019a0bba3dd3a55e2867dbb9a09203f13c2683adf867094637c405ed1&scene=21#wechat_redirect\" textvalue=\"2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\"><span style=\"font-size: 14px;\">2.\u6bd4blast\u8fd8\u4f18\u79c0\u7684\u5e8f\u5217\u6bd4\u5bf9\u5de5\u5177\uff1fHMMER\u6765\u4e86<\/span><\/a><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491909&idx=1&sn=902e34bcf53e605fba2b457ec6a33e36&chksm=cf7f7180f808f8961542f458a49da14e85d8831449fb65fbf2623d55affc564686a5422f56fd&scene=21#wechat_redirect\" textvalue=\"3.\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u6beb\u65e0\u5934\u7eea\uff1f\u8ba9popsicleR\u9886\u4f60\u5165\u95e8\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" style=\"font-size: 14px;\" rel=\"noopener\"><span style=\"font-size: 14px;\">3.\u5bf9\u5355\u7ec6\u80de\u5206\u6790\u6beb\u65e0\u5934\u7eea\uff1f\u8ba9popsicleR\u9886\u4f60\u5165\u95e8<\/span><\/a><\/section>\n<section style=\"letter-spacing: 0.578px;line-height: 1.75em;\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247491905&idx=1&sn=fb34ebd6282962c7803badaee7a39096&chksm=cf7f7184f808f8929608c0050344ad86193d0fc6455c1c18e16cc17bf4b37832b63d3b18284e&scene=21#wechat_redirect\" textvalue=\"4.\u5c0f\u679c\u5e26\u4f60\u7ed8\u5236ROC\u66f2\u7ebf\u8bc4\u4f30\u751f\u5b58\u9884\u6d4b\u80fd\u529b\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"2\" rel=\"noopener\"><span style=\"font-size: 14px;\">4.\u5c0f\u679c\u5e26\u4f60\u7ed8\u5236ROC\u66f2\u7ebf\u8bc4\u4f30\u751f\u5b58\u9884\u6d4b\u80fd\u529b<\/span><\/a><\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"text-align: left;\"><span style=\"font-size: 14px;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;\"><span style=\"font-size: 14px;color: rgb(51, 51, 51);\"><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247493633&idx=1&sn=2263dfe7572c0bcf6816c2c1a37d79de&chksm=cf7f78c4f808f1d2209321d6ace39fde5fa60c0691b56f88eac21916f5a2872ce8ee345f1d5f&scene=21#wechat_redirect\" textvalue=\"\u4f60\u5df2\u9009\u4e2d\u4e86\u6dfb\u52a0\u94fe\u63a5\u7684\u5185\u5bb9\" linktype=\"text\" imgurl=\"\" imgdata=\"null\" data-itemshowtype=\"0\" tab=\"innerlink\" data-linktype=\"1\" rel=\"noopener\"><span class=\"js_jump_icon h5_image_link\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.4255555555555556\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/10_3enDMf2LD6pjia3zQolKXIfTwuh6AA.jpg?w=640\" 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