{"id":53993,"date":"2024-06-16T13:32:03","date_gmt":"2024-06-16T05:32:03","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=53993"},"modified":"2024-06-16T13:32:03","modified_gmt":"2024-06-16T05:32:03","slug":"tidybulk-%e6%91%88%e5%bc%83%e7%b9%81%e7%90%90%e4%bb%a3%e7%a0%81%ef%bc%8c%e5%9c%a8%e5%b7%a8%e4%ba%ba%e8%82%a9%e8%86%80%e5%ad%a6%e4%b9%a0%e8%bd%ac%e5%bd%95%e7%bb%84%ef%bc%88%e4%b8%80%ef%bc%89-4","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=53993","title":{"rendered":"tidybulk\u2014\u6448\u5f03\u7e41\u7410\u4ee3\u7801\uff0c\u5728\u5de8\u4eba\u80a9\u8180\u5b66\u4e60\u8f6c\u5f55\u7ec4\uff08\u4e00\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 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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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rich_media_meta_text\">\u5c0f\u679c  <\/span><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c  <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-12-13 19:00:45<\/em><\/div>\n<p><content><\/p>\n<div class=\"topic\">\n<p>\u6536\u5f55\u4e8e\u8bdd\u9898<\/p>\n<p><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><\/p>\n<\/div>\n<p data-mpa-powered-by=\"yiban.io\"><span style=\"letter-spacing: 0.034em;font-family: \u5b8b\u4f53;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-size: 15px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013555\" data-ratio=\"0.23333333333333334\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_rE2v0O5WiaUDJjgv5bxK2G1ePHyH2g-19.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAysHY49vPGCraibakiaNq6hQgn8C5MfvVLQGxlNZPEia2PajKAzrE2v0O5WiaUDJjgv5bxK2G1ePHyH2g\/640?wx_fmt=jpeg'\" data-type=\"jpeg\" data-w=\"1080\" style=\"letter-spacing: 0.578px;text-align: center;\">\u76f8\u4fe1\u5404\u4f4d\u8fdb\u884c\u751f\u4fe1\u7814\u7a76\u7684\u5c0f\u4f19\u4f34\u4eec\u6216\u591a\u6216\u5c11\u90fd\u542c\u8bf4\u8fc7tidyverse\u8fd9\u4e2aR\u5305\uff0ctidy\u4e3b\u6253\u4e00\u4e2a\u7b80\u5355\u5feb\u6377\uff0c\u5c0f\u679c\u4e4b\u524d\u8fd8\u4ecb\u7ecd\u8fc7tidymodel\u5305\uff0c\u662f\u4e00\u4e2a\u5173\u4e8e\u673a\u5668\u5b66\u4e60\u7684R\u5305\uff0c\u6709\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u5728\u516c\u4f17\u53f7\u8fdb\u884c\u641c\u7d22\u5b66\u4e60\u54e6\u3002\u8a00\u5f52\u6b63\u4f20\uff0ctidy\u662f\u4e00\u4e2a\u5f88\u91cd\u8981\u7684\u7f16\u7a0b\u601d\u60f3\uff0c\u5728\u5199\u4ee3\u7801\u7684\u8fc7\u7a0b\u4e2d\uff0c\u8981\u6c42\u7684\u5c31\u662f\u51cf\u5c11\u4ee3\u7801\u7684\u5197\u4f59\u548c\u6613\u8bfb\u6027\u3002\u5bf9\u4e8e\u65b0\u5165\u95e8\u7684\u5c0f\u4f19\u4f34\u800c\u8a00\u66f4\u662f\u5982\u6b64\uff0c\u4e0d\u4ec5\u53ef\u4ee5\u5e2e\u52a9\u6211\u4eec\u8dd1\u51fa\u7ed3\u679c\u589e\u5f3a\u81ea\u4fe1\u5fc3\uff0c\u8fd8\u53ef\u4ee5\u51cf\u8f7b\u6211\u4eec\u5b66\u4e60\u5927\u91cf\u4ee3\u7801\u6240\u82b1\u8d39\u7684\u65f6\u95f4\u3002\u800c\u4eca\u5929\u5c0f\u679c\u7ed9\u5927\u5bb6\u5206\u4eab\u7684\u4e5f\u662ftidy\u7cfb\u5217\u7684\u4e00\u6b3eR\u5305\uff0c\u800c\u8fd9\u4e2aR\u5305\u4e3b\u8981\u7684\u65b9\u5411\u4fbf\u662f\u8f6c\u5f55\u7ec4\u7684\u5206\u6790\u6d41\u7a0b\uff0c\u800c\u8fd9\u4e2a\u5305\u5c31\u662ftidybulk\uff01\u5c0f\u679c\u4e5f\u660e\u767d\u73b0\u5728\u5927\u5bb6\u7684\u7814\u7a76\u70ed\u70b9\u90fd\u5728\u5355\u7ec6\u80de\u7684\u8f6c\u5f55\u7ec4\u5206\u6790\uff0c\u4f46\u5728\u5b66\u4e60\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u4e4b\u524d\uff0c\u5b66\u4e60\u4e86\u89e3bulk\u8f6c\u5f55\u7ec4\u662f\u80fd\u5f88\u597d\u7684\u5960\u5b9a\u57fa\u7840\u7684\uff01\u56e0\u4e3a\u4e24\u4e2a\u7ec4\u5b66\u7684\u57fa\u8c03\u90fd\u662f\u8f6c\u5f55\u7ec4\u5206\u6790\uff0c\u53ea\u4e0d\u8fc7\u5355\u7ec6\u80de\u8f6c\u5f55\u7ec4\u66f4\u4e3a\u7279\u6b8a\u4e00\u4e9b\uff0c\u4f7f\u7528\u7684\u5177\u4f53\u7b97\u6cd5\u4e0d\u592a\u4e00\u6837\uff0c\u9700\u8981\u8fdb\u884c\u66f4\u6362\u3002\u90a3\u4e48\u80cc\u666f\u77e5\u8bc6\u5c0f\u679c\u5c31\u8bb2\u5230\u8fd9\u5566\uff01\u63a5\u4e0b\u8ba9\u5c0f\u679c\u5e26\u9886\u5927\u5bb6\u5f00\u59cb\u4eca\u5929\u7684\u5b66\u4e60\u5427\uff01\u4ee3\u7801\u57fa\u672c\u90fd\u6765\u81eatidybulk\u7684\u5b98\u7f51\uff08<\/span><span style=\"font-family: Cambria;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;font-size: 15px;\">https:\/\/github.com\/stemangiola\/tidybulk<\/span><span style=\"font-size: 15px;letter-spacing: 0.034em;font-family: \u5b8b\u4f53;font-variant-numeric: normal;font-variant-east-asian: normal;font-variant-alternates: normal;font-variant-position: normal;\">\uff09\uff0c\u6709\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u4e5f\u53ef\u4ee5\u4e0a\u5b98\u7f51\u770b\u770b\u54e6\u3002<br \/><\/span><\/p>\n<h1><span style=\"color: rgb(64, 118, 0);color: rgb(64, 118, 0);font-size: 15px;color: rgb(64, 118, 0);font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u5b89\u88c5\u4e0e\u52a0\u8f7dR\u5305   <\/strong><\/span><\/h1>\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=\"sql\"><code><span class=\"code-snippet_outer\">if(!require(tidybulk)) BiocManager::<span class=\"code-snippet__keyword\">install<\/span>(<span class=\"code-snippet__string\">\"tidybulk\"<\/span>) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(tidyverse) <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(tidybulk) <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">library<\/span>(SummarizedExperiment)<\/span><\/code><\/pre>\n<\/section>\n<h1><span style=\"color: rgb(64, 118, 0);color: rgb(64, 118, 0);font-size: 15px;color: rgb(64, 118, 0);font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u793a\u4f8b\u6570\u636e<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\">\u9996\u5148\u5148\u8ba9\u6211\u4eec\u4e00\u8d77\u6765\u770b\u770b\u793a\u4f8b\u6570\u636e\uff0c\u5728tidybulk\u5305\u4e2d\uff0c\u6211\u4eec\u7814\u7a76\u7684\u5bf9\u8c61\u90fd\u662fSummarizedExperiment\u5bf9\u8c61\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<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=\"shell\"><code><span class=\"code-snippet_outer\">data(counts_SE) <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># class: SummarizedExperiment <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># dim: 8513 48 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># metadata(0): <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># assays(1): count <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># rownames(8513): A1BG A1BG-AS1 ... ZZEF1 ZZZ3 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># rowData names(0): <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># colnames(48): SRR1740034 SRR1740035 ... SRR1740088 SRR1740089 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># colData names(5): Cell.type time condition batch factor_of_interest<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">class(counts_SE)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [1] \"SummarizedExperiment\" <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># attr(,\"package\") <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [1] \"SummarizedExperiment\"<\/span><\/span><\/code><\/pre>\n<\/section>\n<h1><span style=\"color: rgb(64, 118, 0);color: rgb(64, 118, 0);font-size: 15px;color: rgb(64, 118, 0);font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u83b7\u53d6\u8f6c\u5f55\u7ec4\u5206\u6790\u6d41\u7a0b\u7684\u6587\u732e<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u901a\u8fc7get_bibliography()\u51fd\u6570\uff0c\u53ef\u4ee5\u76f4\u63a5\u8f93\u51fa\u5206\u6790\u6d41\u7a0b\u4e2d\u7684\u6587\u732e\uff0c\u8fd9\u5bf9\u5404\u4f4d\u5c0f\u4f19\u4f34\u64b0\u5199\u8bba\u6587\uff0c\u6216\u662f\u8fdb\u884c\u6df1\u4e00\u5c42\u5b66\u4e60\u90fd\u662f\u6781\u5176\u65b9\u4fbf\u7684\u4e00\u4e2a\u529f\u80fd\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">counts_SE %>%get_bibliography()<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># @Article{tidybulk, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># title = {tidybulk: an R tidy framework for modular transcriptomic data analysis}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># author = {Stefano Mangiola and Ramyar Molania and Ruining Dong and Maria A. Doyle & Anthony T. Papenfuss}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># journal = {Genome Biology}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># year = {2021}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># volume = {22}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># number = {42}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># url = {https:\/\/genomebiology.biomedcentral.com\/articles\/10.1186\/s13059-020-02233-7}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># } <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># @article{wickham2019welcome, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># title={Welcome to the Tidyverse}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># author={Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and Francois, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and others}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># journal={Journal of Open Source Software}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># volume={4}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># number={43}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># pages={1686}, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># year={2019} <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># }<\/span><\/span><\/code><\/pre>\n<\/section>\n<h1><span style=\"color: rgb(64, 118, 0);color: rgb(64, 118, 0);font-size: 15px;color: rgb(64, 118, 0);font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u6574\u5408\u91cd\u590d\u7684\u8f6c\u5f55\u672c<\/strong><\/span><span style=\"font-size: 15px;\"><br \/>\n  <\/span><\/h1>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5728\u6211\u4eec\u7684\u7814\u7a76\u4e2d\uff0c\u6211\u4eec\u65f6\u5e38\u4f1a\u9047\u5230\u57fa\u56e0\u540d\uff0cENSEMBLE\u7f16\u53f7\u7b49\u8fdb\u884c\u4e92\u6362\u7684\u60c5\u51b5\uff0c\u4f46\u5927\u591a\u6570\u65f6\u5019\u4ed6\u4eec\u7684\u5173\u7cfb\u5e76\u4e0d\u662f\u4e00\u4e00\u5bf9\u5e94\u7684\u3002\u8fd9\u79cd\u65f6\u5019\uff0c\u6211\u4eec\u5c31\u5fc5\u987b\u5904\u7406\u91cd\u590d\u9879\uff0c\u5c0f\u679c\u4eca\u5929\u4ecb\u7ecd\u7684R\u5305\u5c31\u6709\u8fd9\u4e48\u4e00\u4e2a\u51fd\u6570\uff0caggregate_duplicates\u51fd\u6570\u53ef\u4ee5\u5c06tibble\u548c\u5217\u540d\u4f5c\u4e3a\u53c2\u6570\u8fdb\u884c\u6574\u5408\uff0c\u4e00\u8d77\u6765\u770b\u770b\u4e0b\u9762\u7684\u4f8b\u5b50\u3002<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">rowData(counts_SE)$<\/span>gene_name =rownames(counts_SE) <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.aggr = counts_SE %>%aggregate_duplicates(.transcript = gene_name) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">dim(counts_SE)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [1] 8513 48<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">dim(counts_SE.aggr)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [1] 8513 48<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u901a\u8fc7\u7ef4\u5ea6\u7684\u6bd4\u8f83\u6211\u4eec\u770b\u4e0d\u51fa\u5dee\u522b\uff0c\u8fd9\u662f\u56e0\u4e3a\u5728\u8fd9\u4e2a\u793a\u4f8b\u4e2d\uff0c\u5c0f\u679c\u4f7f\u7528\u7684\u662f\u884c\u540d\uff0c\u884c\u540d\u672c\u6765\u5c31\u662f\u6ca1\u6709\u91cd\u590d\u7684\u54a7\uff0c\u6240\u4ee5\u6211\u4eec\u6362\u4e2a\u65b9\u6cd5\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u8fd9\u91cc\u5c0f\u679c\u53d6\u4e00\u4e2a\u6781\u7aef\u4e00\u70b9\u7684\u4f8b\u5b50\u54e6\uff0c\u6211\u4eec\u5047\u8bbea\uff0cb\uff0cc\uff0cd\u662f\u4e0d\u540c\u7684\u7f16\u53f7\uff0c\u4f7f\u7528\u540c\u6837\u7684\u65b9\u6848\u8fdb\u884c\u6574\u5408 <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">rowData(counts_SE)$<\/span>gene_name =c(<span class=\"code-snippet__string\">\"a\"<\/span>,<span class=\"code-snippet__string\">\"b\"<\/span>,<span class=\"code-snippet__string\">\"c\"<\/span>,rep(<span class=\"code-snippet__string\">\"d\"<\/span>,8510)) <\/span><\/code><code><span class=\"code-snippet_outer\">tmp = counts_SE %>%aggregate_duplicates(.transcript = gene_name) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">dim(tmp)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [1] 4 48<\/span><\/span><\/code><\/pre>\n<\/section>\n<h1><span style=\"color: rgb(64, 118, 0);color: rgb(64, 118, 0);font-size: 15px;color: rgb(64, 118, 0);font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u6807\u51c6\u5316<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u5728\u8f6c\u5f55\u7ec4\u7684\u5206\u6790\u8fc7\u7a0b\u4e2d\uff0c\u6211\u4eec\u9700\u8981\u5c06\u8f6c\u5f55\u672c\u7684\u4e30\u5ea6\u8fdb\u884c\u6807\u51c6\u5316\u5904\u7406\uff0c\u8fd9\u4e5f\u662f\u4e3a\u4e86\u4fbf\u4e8e\u540e\u7eed\u7684\u5206\u6790\u5904\u7406\u3002<\/span><span style=\"background-color: rgb(248, 248, 248);color: rgb(143, 89, 2);font-family: Consolas;font-style: italic;font-size: 15px;text-align: left;text-indent: 0pt;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<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=\"shell\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u5c0f\u679c\u8fd9\u91cc\u89e3\u91ca\u4e00\u4e0b\u4ee3\u7801\u54e6~ \u9996\u5148\u7b5b\u9009\u51fa\u5728\u4e0d\u540c\u6761\u4ef6\u4e0b\u4e30\u5ea6\u663e\u8457\u4e0d\u540c\u7684\u8f6c\u5f55\u672c\uff0c\u7136\u540e\u4f7f\u7528\u4e86scale_abundance()\u51fd\u6570\u8fdb\u884c\u6807\u51c6\u5316\u3002 <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm = counts_SE.aggr %>%identify_abundant(factor_of_interest = condition) %>%scale_abundance() <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">assays(counts_SE.norm) %>%names() <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [1] \"count\" \"count_scaled\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u8fd9\u91cc\u53ef\u4ee5\u89c2\u5bdf\u5230\uff0c\u6807\u51c6\u5316\u8fc7\u540e\u589e\u52a0\u4e86\u4e00\u4e2aassay\u7684\u77e9\u9635 <\/span><\/code><code><span class=\"code-snippet_outer\">assay(counts_SE.norm,\"count_scaled\")[1:5,1:5]<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># SRR1740034 SRR1740035 SRR1740036 SRR1740037 SRR1740038 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># A1BG 238.8192 312.8522 259.1186 206.4091 149.54205 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># A1BG-AS1 129.5555 134.4972 118.2644 124.1811 36.59008 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># AAAS 1354.8695 1478.0076 1360.7047 1246.8449 1094.52054 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># AACS 346.5219 400.5678 406.6168 354.0838 174.99602 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># AAGAB 920.9366 881.5416 968.7048 1023.6547 1374.51416<\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u5c0f\u679c\u901a\u8fc7\u8fd9\u884c\u4ee3\u7801\u5c06\u6807\u51c6\u5316\u8fc7\u540e\u7684\u77e9\u9635\u5c55\u73b0\u7ed9\u5404\u4f4d\u5c0f\u4f19\u4f34\u770b\u770b\u3002 <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">tbl <- tidySummarizedExperiment::as_tibble(counts_SE.norm) <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u8fd9\u91cc\u5c0f\u679c\u81ea\u5df1\u9047\u5230\u4e86\u4e00\u4e2abug\u54e6\uff0c\u521a\u5f00\u59cb\u7684\u65f6\u5019\u4e00\u76f4\u8f6c\u6362\u4e0d\u6210\u529f\uff0c\u7ecf\u8fc7\u7814\u7a76\u540e\u53d1\u73b0\u9700\u8981\u4e0b\u8f7d\u8fd9\u4e2aR\u5305 <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u53ef\u4ee5\u4f7f\u7528BiocManger\u8fdb\u884c\u4e0b\u8f7d\u54e6 <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> BiocManager::install(<span class=\"code-snippet__string\">\"tidySummarizedExperiment\"<\/span>) <\/span><\/code><code><span class=\"code-snippet_outer\">head(tbl)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A tibble: 6 \u00d7 13 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># .feature .sample count count_scaled Cell.type time condition batch <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 A1BG SRR1740034 153 239. b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 A1BG-AS1 SRR1740034 83 130. b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 AAAS SRR1740034 868 1355. b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 AACS SRR1740034 222 347. b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 AAGAB SRR1740034 590 921. b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 AAMDC SRR1740034 48 74.9 b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 5 more variables: factor_of_interest, TMM, multiplier, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # gene_name, .abundant<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">names(tbl)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [1] \".feature\" \".sample\" \"count\" <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [4] \"count_scaled\" \"Cell.type\" \"time\" <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [7] \"condition\" \"batch\" \"factor_of_interest\" <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [10] \"TMM\" \"multiplier\" \"gene_name\" <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># [13] \".abundant\" <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u5bf9\u6807\u51c6\u5316\u7684\u7ed3\u679c\u8fdb\u884c\u53ef\u89c6\u5316 <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> ggplot(aes(count_scaled +1, group=.sample, color=Cell.type)) + <\/span><\/code><code><span class=\"code-snippet_outer\"> geom_density() + <\/span><\/code><code><span class=\"code-snippet_outer\"> scale_x_log10() + <\/span><\/code><code><span class=\"code-snippet_outer\"> scale_fill_brewer(palette =\"Set3\") + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme_bw()<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013551\" data-ratio=\"0.8\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_guEbyaQPN4FPBN7U06qMvib1E9X5ng-3.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXJe7mmOiblVFjicxzEuPW1vpYibkBguEbyaQPN4FPBN7U06qMvib1E9X5ng\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"384.780029296875\" width=\"480.969970703125\" \/><\/span><\/p>\n<h1><span style=\"color: rgb(64, 118, 0);color: rgb(64, 118, 0);font-size: 15px;color: rgb(64, 118, 0);font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u7b5b\u9009\u53d8\u5f02\u57fa\u56e0<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;font-size: 15px;\">\u8f6c\u5f55\u7ec4\u7684\u5206\u6790\uff0c\u6211\u4eec\u9996\u8981\u7684\u76ee\u7684\u5c31\u662f\u60f3\u627e\u51fa\u5dee\u5f02\u561b\uff0c\u800c\u8fd9\u4e00\u6b65\u5c31\u662f\u7b5b\u9009\u51fa\u5dee\u5f02\u57fa\u56e0\u3002<\/span><span style=\"background-color: rgb(248, 248, 248);font-family: Consolas;font-size: 15px;text-align: left;text-indent: 0pt;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<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=\"shell\"><code><span class=\"code-snippet_outer\">counts_SE.norm.variable = counts_SE.norm %>%keep_variable(top =100) # \u5c0f\u679c\u8fd9\u91cc\u901a\u8fc7top\u53c2\u6570\u4ec5\u4fdd\u7559\u4e86\u524d100\u57fa\u56e0\u3002 <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">head(counts_SE.norm.variable)<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A SummarizedExperiment-tibble abstraction: 288 \u00d7 48 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # [90mFeatures=6 | Samples=48 | Assays=count, count_scaled[0m <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># .feature .sample count count_scaled Cell.type time condition batch <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 SERPINA1 SRR1740034 4 6.24 b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 CSF3R SRR1740034 4 6.24 b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 TNFAIP2 SRR1740034 4 6.24 b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 S100A9 SRR1740034 16 25.0 b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 VCAN SRR1740034 8 12.5 b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 C5AR1 SRR1740034 2 3.12 b_cell 0 d TRUE 0 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 7 SERPINA1 SRR1740035 4 5.85 b_cell 1 d TRUE 1 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 8 CSF3R SRR1740035 12 17.5 b_cell 1 d TRUE 1 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 9 TNFAIP2 SRR1740035 11 16.1 b_cell 1 d TRUE 1 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 10 S100A9 SRR1740035 15 21.9 b_cell 1 d TRUE 1 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 110 more rows <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 5 more variables: factor_of_interest, TMM, multiplier, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # gene_name, .abundant <\/span><\/span><\/code><\/pre>\n<\/section>\n<h1><span style=\"font-size: 15px;\"><span style=\"font-family: \u5b8b\u4f53;font-variant: normal;text-transform: none;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-imgfileid=\"100013596\" data-ratio=\"0.38981481481481484\" data-s=\"300,640\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_IWicymEetCc6Enf2BkUE4Yz1Ya5e5w-3.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAyuYsqlJnQUJvnS2iciaDibtfbdV0VmHlriaSjYwjFPLp1BLjokHIWicymEetCc6Enf2BkUE4Yz1Ya5e5w\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" style=\"font-size: 15px;letter-spacing: 0.578px;text-wrap: wrap;font-family: "Helvetica Neue", Helvetica, "Hiragino Sans GB", "Microsoft YaHei", Arial, sans-serif;text-align: center;\" \/><\/span><\/span><\/h1>\n<h1><span style=\"color: rgb(64, 118, 0);color: rgb(64, 118, 0);font-size: 15px;color: rgb(64, 118, 0);font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>\u964d\u7ef4<br \/>\n  <\/strong><\/span><\/h1>\n<p><span style=\"font-size: 15px;font-family: Cambria;font-variant: normal;text-transform: none;\">tidybulk\u5305\u4e2d\u96c6\u5408\u4e86\u4e09\u79cd\u964d\u7ef4\u7684\u7b97\u6cd5\uff0c\u4ed6\u4eec\u5206\u522b\u662fMDS\uff0cPCA\u548ctSNE\uff0c\u5404\u4f4d\u5c0f\u4f19\u4f34\u53ef\u4ee5\u6839\u636e\u9700\u6c42\u8fdb\u884c\u9009\u62e9\u3002\u5c0f\u679c\u5728\u8fd9\u5bf9\u4e09\u79cd\u7b97\u6cd5\u90fd\u8fdb\u884c\u4e00\u904d\u6f14\u793a\u3002## MDS<\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<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=\"shell\"><code><span class=\"code-snippet_outer\">counts_SE.norm.MDS = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE.norm %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> reduce_dimensions(method=\"MDS\", .dims =6) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.MDS %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> pivot_sample() %>%# \u4fdd\u7559\u6837\u672c\u76f8\u5173\u7684\u5217\uff0c\u8fd9\u6837\u53ef\u4ee5\u51cf\u5c11\u8ba1\u7b97\u7684\u65f6\u95f4\u3002 <\/span><\/code><code><span class=\"code-snippet_outer\"> select(contains(\"Dim\"), everything()) # \u901a\u8fc7\u8fd9\u884c\u4ee3\u7801\u53ef\u4ee5\u51cf\u5c11\u5217\u7684\u987a\u5e8f\u3002<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A tibble: 48 \u00d7 14 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Dim1 Dim2 Dim3 Dim4 Dim5 Dim6 .sample Cell.type time <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 -1.46 0.220 -1.68 0.0553 0.0658 -0.126 SRR1740034 b_cell 0 d <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 -1.46 0.226 -1.71 0.0300 0.0454 -0.137 SRR1740035 b_cell 1 d <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 -1.44 0.193 -1.60 0.0890 0.0503 -0.121 SRR1740036 b_cell 3 d <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 -1.44 0.198 -1.67 0.0891 0.0543 -0.110 SRR1740037 b_cell 7 d <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 0.243 -1.42 0.182 0.00642 -0.503 -0.131 SRR1740038 dendritic_mye\u2026 0 d <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 0.191 -1.42 0.195 0.0180 -0.457 -0.130 SRR1740039 dendritic_mye\u2026 1 d <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 7 0.257 -1.42 0.152 0.0130 -0.582 -0.0927 SRR1740040 dendritic_mye\u2026 3 d <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 8 0.162 -1.43 0.189 0.0232 -0.452 -0.109 SRR1740041 dendritic_mye\u2026 7 d <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 9 0.516 -1.47 0.240 -0.251 0.457 -0.119 SRR1740042 monocyte 0 d <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 10 0.514 -1.41 0.231 -0.219 0.458 -0.131 SRR1740043 monocyte 1 d <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 38 more rows <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 5 more variables: condition, batch, factor_of_interest, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # TMM, multiplier <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span> \u5c0f\u679c\u5c0fTips\uff1a\u5728\u8fd9\u9700\u8981\u5b89\u88c5\u4e00\u4e2aR\u5305\u54e6~ <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># install.packages(\"GGally\") <\/span><\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.MDS %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> pivot_sample() %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> GGally::ggpairs(columns =6:(6+5), ggplot2::aes(colour=`Cell.type`))<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013553\" data-ratio=\"0.8\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_TUjibIWVFQfZl4EkX3QjickbpH1l3Q-3.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXJNYeezUW01XGH8JlURgFkQSIdzTUjibIWVFQfZl4EkX3QjickbpH1l3Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"384.77996826171875\" width=\"480.969970703125\" \/><\/span><\/p>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"apache\"><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__comment\"># \u8fd9\u4e2a\u56fe\u5c31\u662f\u5404\u7ef4\u5ea6\u4e4b\u95f4\u7684\u76f8\u5173\u5173\u7cfb\u5566<\/span><\/span><\/code><\/pre>\n<\/section>\n<h2><span style=\"color: rgb(64, 118, 0);color: rgb(64, 118, 0);font-size: 15px;color: rgb(64, 118, 0);font-family: Calibri;font-variant: normal;text-transform: none;\"><strong>PCA   <\/strong><\/span><\/h2>\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<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"shell\"><code><span class=\"code-snippet_outer\">counts_SE.norm.PCA = <\/span><\/code><code><span class=\"code-snippet_outer\"> counts_SE.norm %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> reduce_dimensions(method=\"PCA\", .dims =6) <\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"><br \/><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.PCA %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> pivot_sample() %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> select(contains(\"PC\"), everything())<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A tibble: 48 \u00d7 14 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># PC1 PC2 PC3 PC4 PC5 PC6 .sample Cell.type time condition <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"> <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 -12.6 -2.52 -14.9 -0.424 -0.592 -1.22 SRR17400\u2026 b_cell 0 d TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 -12.6 -2.57 -15.2 -0.140 -0.388 -1.30 SRR17400\u2026 b_cell 1 d TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 -12.6 -2.41 -14.5 -0.714 -0.344 -1.10 SRR17400\u2026 b_cell 3 d TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 -12.5 -2.34 -14.9 -0.816 -0.427 -1.00 SRR17400\u2026 b_cell 7 d TRUE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 0.189 13.0 1.66 -0.0269 4.64 -1.35 SRR17400\u2026 dendriti\u2026 0 d FALSE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 -0.293 12.9 1.76 -0.0727 4.21 -1.28 SRR17400\u2026 dendriti\u2026 1 d FALSE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 7 0.407 13.0 1.42 -0.0529 5.37 -1.01 SRR17400\u2026 dendriti\u2026 3 d FALSE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 8 -0.620 13.0 1.73 -0.201 4.17 -1.07 SRR17400\u2026 dendriti\u2026 7 d FALSE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 9 2.56 13.5 2.32 2.03 -4.32 -1.22 SRR17400\u2026 monocyte 0 d FALSE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 10 2.65 13.1 2.21 1.80 -4.29 -1.30 SRR17400\u2026 monocyte 1 d FALSE <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 38 more rows <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 4 more variables: batch, factor_of_interest, TMM, <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # multiplier <\/span><\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.PCA %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> pivot_sample() %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> GGally::ggpairs(columns =11:13, ggplot2::aes(colour=`Cell.type`))<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013552\" data-ratio=\"0.8\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_K4CPIoiamlTRYZkIkSoKg1NRwbtL6Q-3.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXnib5BwtQsGah9pKQSEPcib4Z1xGK4CPIoiamlTRYZkIkSoKg1NRwbtL6Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"384.780029296875\" width=\"480.969970703125\" \/><\/span><\/p>\n<h2><span style=\"color: rgb(64, 118, 0);\"><strong><span style=\"color: rgb(64, 118, 0);font-size: 15px;\"><span style=\"color: rgb(64, 118, 0);font-family: Calibri;font-variant: normal;text-transform: none;\">tSNE<\/span> <\/span><\/strong><\/span><\/h2>\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<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=\"shell\"><code><span class=\"code-snippet_outer\">counts_SE.norm.tSNE = <\/span><\/code><code><span class=\"code-snippet_outer\"> breast_tcga_mini_SE %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> identify_abundant() %>%# \u7b5b\u9009\u9ad8\u8868\u8fbe\u7684\u7279\u5f02\u57fa\u56e0 <\/span><\/code><code><span class=\"code-snippet_outer\"> reduce_dimensions( <\/span><\/code><code><span class=\"code-snippet_outer\"> method =\"tSNE\", <\/span><\/code><code><span class=\"code-snippet_outer\"> perplexity=10, <\/span><\/code><code><span class=\"code-snippet_outer\"> pca_scale =TRUE <\/span><\/code><code><span class=\"code-snippet_outer\"> ) <\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Performing PCA <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Read the 251 x 50 data matrix successfully! <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># OpenMP is working. 1 threads. <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Using no_dims = 2, perplexity = 10.000000, and theta = 0.500000 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Computing input similarities... <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Building tree... <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Done in 0.02 seconds (sparsity = 0.182886)! <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Learning embedding... <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 50: error is 67.381499 (50 iterations in 0.03 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 100: error is 68.239243 (50 iterations in 0.04 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 150: error is 69.030962 (50 iterations in 0.03 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 200: error is 69.041501 (50 iterations in 0.04 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 250: error is 67.702680 (50 iterations in 0.05 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 300: error is 1.540607 (50 iterations in 0.04 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 350: error is 1.193476 (50 iterations in 0.02 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 400: error is 1.146808 (50 iterations in 0.02 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 450: error is 1.135869 (50 iterations in 0.02 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 500: error is 1.121872 (50 iterations in 0.01 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 550: error is 1.119940 (50 iterations in 0.01 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 600: error is 1.115307 (50 iterations in 0.01 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 650: error is 1.110707 (50 iterations in 0.01 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 700: error is 1.108459 (50 iterations in 0.01 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 750: error is 1.102872 (50 iterations in 0.01 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 800: error is 1.099258 (50 iterations in 0.02 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 850: error is 1.095792 (50 iterations in 0.01 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 900: error is 1.093945 (50 iterations in 0.01 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 950: error is 1.092175 (50 iterations in 0.01 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Iteration 1000: error is 1.091423 (50 iterations in 0.01 seconds) <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># Fitting performed in 0.44 seconds.<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.tSNE %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> pivot_sample() %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> select(contains(\"tSNE\"), everything())<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # A tibble: 251 \u00d7 4 <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># tSNE1 tSNE2 .sample Call <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 1 3.33 9.32 TCGA-A1-A0SD-01A-11R-A115-07 LumA <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 2 -3.49 -5.36 TCGA-A1-A0SF-01A-11R-A144-07 LumA <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 3 -0.759 15.4 TCGA-A1-A0SG-01A-11R-A144-07 LumA <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 4 -3.82 7.05 TCGA-A1-A0SH-01A-11R-A084-07 LumA <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 5 0.670 6.59 TCGA-A1-A0SI-01A-11R-A144-07 LumB <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 6 -1.38 13.0 TCGA-A1-A0SJ-01A-11R-A084-07 LumA <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 7 -9.85 -33.5 TCGA-A1-A0SK-01A-12R-A084-07 Basal <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 8 -12.1 9.13 TCGA-A1-A0SM-01A-11R-A084-07 LumA <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 9 -10.9 9.79 TCGA-A1-A0SN-01A-11R-A144-07 LumB <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># 10 1.61 23.2 TCGA-A1-A0SQ-01A-21R-A144-07 LumA <\/span><\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__meta\">#<\/span><span class=\"code-snippet__comment\"># # \u2139 241 more rows <\/span><\/span><\/code><code><span class=\"code-snippet_outer\">counts_SE.norm.tSNE %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> pivot_sample() %>% <\/span><\/code><code><span class=\"code-snippet_outer\"> ggplot(aes(x =`tSNE1`, y =`tSNE2`, color=Call)) + <\/span><\/code><code><span class=\"code-snippet_outer\"> geom_point() + <\/span><\/code><code><span class=\"code-snippet_outer\"> theme_bw()<\/span><\/code><\/pre>\n<\/section>\n<p><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" loading=\"lazy\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013554\" data-ratio=\"0.8\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_8wqrFUfJ5hsibDhlc2eA6CsYtsYibg-3.png\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_png\/zcicibWZessAwQz0aWHeCNyvlBdpqE9icxXdH1kXRW3JXiaZ9eJc6BUPPl6MZJ8wqrFUfJ5hsibDhlc2eA6CsYtsYibg\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"1080\" height=\"384.7799987792969\" width=\"480.969970703125\" \/> \u8fd9\u4ee5\u4e0a\u5c31\u662f\u8f6c\u5f55\u7ec4\u5206\u6790\u7684\u524d\u534a\u90e8\u5206\u7684\u5206\u6790\u6d41\u7a0b\u5566\uff0c\u5185\u5bb9\u4e5f\u6709\u70b9\u591a\uff0c\u5c0f\u679c\u4f1a\u5206\u4e3a\u4e24\u7ae0\u8fdb\u884c\u8bb2\u8bc9\u54e6~\u4e5f\u5e0c\u671b\u5404\u4f4d\u5c0f\u4f19\u4f34\u53ef\u4ee5\u5480\u56bc\u5438\u6536\uff0c\u5173\u6ce8\u6211\u4eec\u7684\u516c\u4f17\u53f7\u53d1\u6587\uff0c\u7ed9\u5927\u5bb6\u7a0d\u5fae\u5267\u900f\u4e00\u4e0b\uff0c\u5728\u540e\u534a\u7ae0\u5c0f\u679c\u4f1a\u6559\u5927\u5bb6\u4e30\u5ea6\u5dee\u5f02\uff0c\u673a\u5668\u5b66\u4e60\u63a8\u65ad\u7ec6\u80de\u7ec4\u6210\u7b49\u7b49\u5185\u5bb9\uff0c\u656c\u8bf7\u671f\u5f85\u54e6\uff01<\/span><\/p>\n<p><a target=\"_blank\" href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247497335&idx=2&sn=b9bd1327156243517c611c7c071a2de6&chksm=cf7f66b2f808efa472e6930865ed8da7fbaa600ed58351f035314ce545b26ea32fb9311a8faf&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 style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><span class=\"js_jump_icon h5_image_link\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-imgfileid=\"100013694\" data-ratio=\"0.35444444444444445\" src=\"http:\/\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_thFQOgQyssQC5z0JC8vHib67rtI8DA.jpg\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/sz_mmbiz_jpg\/zcicibWZessAwkToGOGI4N8c4iaZcg02J3icy1xq0FfHysk9tmTIkDIW8ia32uthFQOgQyssQC5z0JC8vHib67rtI8DA\/640?wx_fmt=jpeg&from=appmsg&wxfrom=5&wx_lazy=1&wx_co=1'\" data-w=\"900\" \/><\/span><\/span><\/a><span style=\"font-family: Cambria;font-variant: normal;text-transform: none;font-size: 15px;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" 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