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| title: "听说你想把多个样本的 GSEA 画在一起?" | ||
| date: 2023-09-09T23:36:10Z | ||
| draft: ["false"] | ||
| tags: [ | ||
| "fetched", | ||
| "老俊俊的生信笔记" | ||
| ] | ||
| categories: ["Acdemic"] | ||
| --- | ||
| 听说你想把多个样本的 GSEA 画在一起? by 老俊俊的生信笔记 | ||
| ------ | ||
| <div><section data-tool="mdnice编辑器" data-website="https://www.mdnice.com" data-mpa-powered-by="yiban.io"><h4 data-tool="mdnice编辑器"><span></span></h4><section><mp-common-profile data-pluginname="mpprofile" data-id="MzkyMTI1MTYxNA==" data-headimg="http://mmbiz.qpic.cn/mmbiz_png/G5jjcE4usey42oX5qyLTVibLRO9dz8ic5G4TpEHQc9rICYlpS4MHg6Et8cgXrQDqibvibXombicTro8t9cekJRlDBcw/0?wx_fmt=png" data-nickname="老俊俊的生信笔记" data-alias="JunJunLab" data-signature="老俊俊的生信技能和知识分享,我不是巨人,但你可以站在我的肩膀上更进一步!" data-from="0" data-is_biz_ban="0"></mp-common-profile></section></section><section><qqmusic musicid="125494406" mid="000A0MgV2a12dq" albumurl="http://y.gtimg.cn/music/photo_new/T001R120x120M000003tMm0y0TuewY_3.jpg" audiourl="http://isure6.stream.qqmusic.qq.com/C200003bpSNO2gbhaF.m4a?guid=2000000052&vkey=F5107498AF51962B610B47A6D0CC34479CA98AFEEB9D4F775224A0FCF34F93908C203031EDAD3EE7CD567DE172D91AFBF782D3670740493E&uin=0&fromtag=20052" music_name="我变了我没变" singer="杨宗纬" play_length="435" src="/mp/readtemplate?t=app_editor/music&singer=%E6%9D%A8%E5%AE%97%E7%BA%AC&music_name=%E6%88%91%E5%8F%98%E4%BA%86%E6%88%91%E6%B2%A1%E5%8F%98&albumurl=http%3A%2F%2Fy.gtimg.cn%2Fmusic%2Fphoto_new%2FT001R120x120M000003tMm0y0TuewY_3.jpg&musictype=1" musictype="1" otherid="000A0MgV2a12dq" albumid="" jumpurlkey="" data-pluginname="insertaudio"></qqmusic></section><section data-tool="mdnice编辑器" data-website="https://www.mdnice.com"><h4 data-tool="mdnice编辑器"><span></span></h4><h2 data-tool="mdnice编辑器"><span><span>1</span></span><span>引言</span><span></span></h2><blockquote data-tool="mdnice编辑器"><p>有粉丝提问, <strong>如何把多个组/实验的同一条 GSEA 结果画在一个图里,这样可以查看不同实验条件该通路的变化情况</strong>。本质上就是提取多个通路的富集结果,合并一下数据,然后绘图就好了,写了个简单的函数 <strong>GSEAmultiGP</strong> 来做这样的事情。</p></blockquote><p data-tool="mdnice编辑器"><strong>示例文献图,来自粉丝:</strong></p><figure data-tool="mdnice编辑器"><img data-ratio="0.7769230769230769" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpsX5y4zCib2XQSFDW6sUxjibcvf0Wxha1VoWABayspOl1vrolJD8GqRFQ/640?wx_fmt=png" data-type="png" data-w="780" src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpsX5y4zCib2XQSFDW6sUxjibcvf0Wxha1VoWABayspOl1vrolJD8GqRFQ/640?wx_fmt=png"></figure><p data-tool="mdnice编辑器"><strong>文献题目:</strong></p><blockquote data-tool="mdnice编辑器"><p><strong><em>p53 Mediates Vast Gene Expression Changes That Contribute to Poor Chemotherapeutic Response in a Mouse Model of Breast Cancer</em></strong></p></blockquote><h2 data-tool="mdnice编辑器"><span><span>2</span></span><span>安装</span><span></span></h2><p data-tool="mdnice编辑器">重新安装获取新功能:</p><pre data-tool="mdnice编辑器"><span></span><code><span># install.packages("devtools")</span><br>devtools::install_github(<span>"junjunlab/GseaVis"</span>)<br></code></pre><h2 data-tool="mdnice编辑器"><span><span>3</span></span><span>使用示例</span><span></span></h2><h3 data-tool="mdnice编辑器"><span></span><span>数据准备</span><span></span></h3><p data-tool="mdnice编辑器">先造三个不同的 genelist,代表三个条件下基因的变化:</p><pre data-tool="mdnice编辑器"><span></span><code><span>library</span>(clusterProfiler)<br><span>library</span>(org.Hs.eg.db)<br><span>library</span>(GseaVis)<br><br>data(geneList, package=<span>"DOSE"</span>)<br><br>geneList1 <- sort(sample(seq(-<span>2</span>,<span>2</span>,by = <span>0.01</span>),<span>12495</span>,replace = <span>T</span>),decreasing = <span>T</span>)<br>names(geneList1) <- sample(names(geneList),<span>12495</span>,replace = <span>F</span>)<br><br>geneList2 <- sort(sample(seq(-<span>2</span>,<span>2</span>,by = <span>0.01</span>),<span>12495</span>,replace = <span>T</span>),decreasing = <span>T</span>)<br>names(geneList2) <- sample(names(geneList),<span>12495</span>,replace = <span>F</span>)<br><br><br>all_glist <- list(geneList,geneList1,geneList2)<br></code></pre><p data-tool="mdnice编辑器">然后做 GSEA 富集分析,返回 list,这里设置 <strong>pvalueCutoff=1</strong>,保证在每个富集结果里都有共同的通路:</p><pre data-tool="mdnice编辑器"><span></span><code><span># loop to enrich</span><br>lapply(<span>1</span>:<span>3</span>, <span>function</span>(x){<br> ego3 <- gseGO(geneList = all_glist[[x]],<br> OrgDb = org.Hs.eg.db,<br> ont = <span>"BP"</span>,<br> minGSSize = <span>100</span>,<br> maxGSSize = <span>500</span>,<br> pvalueCutoff = <span>1</span>,<br> verbose = <span>FALSE</span>)<br>}) -> m_gsea_list<br></code></pre><figure data-tool="mdnice编辑器"><img data-ratio="0.25112107623318386" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicp4Z2gkJZLsibEve8bwfFwx1CPKcJRXdoBwEWxt8icyX0dBYMoKWl8CxKQ/640?wx_fmt=png" data-type="png" data-w="669" src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicp4Z2gkJZLsibEve8bwfFwx1CPKcJRXdoBwEWxt8icyX0dBYMoKWl8CxKQ/640?wx_fmt=png"></figure><p data-tool="mdnice编辑器">查看其中一个结果:</p><pre data-tool="mdnice编辑器"><span></span><code><span># check</span><br>df <- data.frame(m_gsea_list[[<span>1</span>]])<br></code></pre><figure data-tool="mdnice编辑器"><img data-ratio="0.26717557251908397" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpF0DmM0pt0qrGIVGt8A4OwcysD05uedLWpGxfUUcS8AsR3shRZ2Yb6g/640?wx_fmt=png" data-type="png" data-w="1441" src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpF0DmM0pt0qrGIVGt8A4OwcysD05uedLWpGxfUUcS8AsR3shRZ2Yb6g/640?wx_fmt=png"></figure><h3 data-tool="mdnice编辑器"><span></span><span>绘图</span><span></span></h3><p data-tool="mdnice编辑器">默认绘图:</p><pre data-tool="mdnice编辑器"><span></span><code><span># plot</span><br>GSEAmultiGP(gsea_list = m_gsea_list,<br> geneSetID = <span>"GO:0002757"</span>,<br> exp_name = c(<span>"group1"</span>,<span>"group2"</span>,<span>"group3"</span>))<br></code></pre><figure data-tool="mdnice编辑器"><img data-ratio="0.7813953488372093" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpfJ4oZ8ffuTfkl6numGaQal4E0yWXJEicpoEkmrO6uHbiaW9bVvLYiaXLQ/640?wx_fmt=png" data-type="png" data-w="645" src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpfJ4oZ8ffuTfkl6numGaQal4E0yWXJEicpoEkmrO6uHbiaW9bVvLYiaXLQ/640?wx_fmt=png"></figure><p data-tool="mdnice编辑器">修改颜色:</p><pre data-tool="mdnice编辑器"><span></span><code>GSEAmultiGP(gsea_list = m_gsea_list,<br> geneSetID = <span>"GO:0002757"</span>,<br> exp_name = c(<span>"group1"</span>,<span>"group2"</span>,<span>"group3"</span>),<br> curve.col = ggsci::pal_lancet()(<span>3</span>))<br></code></pre><figure data-tool="mdnice编辑器"><img data-ratio="0.772093023255814" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicp2dYYJDQharql5WTdt0CicjBRu3xiafvdLYvMMJicEibCDwGcibzZTL3T8Vg/640?wx_fmt=png" data-type="png" data-w="645" src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicp2dYYJDQharql5WTdt0CicjBRu3xiafvdLYvMMJicEibCDwGcibzZTL3T8Vg/640?wx_fmt=png"></figure><p data-tool="mdnice编辑器">添加 P 值:</p><pre data-tool="mdnice编辑器"><span></span><code>GSEAmultiGP(gsea_list = m_gsea_list,<br> geneSetID = <span>"GO:0002757"</span>,<br> exp_name = c(<span>"group1"</span>,<span>"group2"</span>,<span>"group3"</span>),<br> curve.col = ggsci::pal_d3()(<span>3</span>),<br> addPval = <span>T</span>,<br> pvalX = <span>0.99</span>,pvalY = <span>0.99</span>,<br> legend.position = <span>"right"</span>)<br></code></pre><figure data-tool="mdnice编辑器"><img data-ratio="0.7993779160186625" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpEV3Ct0YPwBZEO1yZfibIRq3djrAeaIIVAZMeibhD7eqskxJF0kMqkbcw/640?wx_fmt=png" data-type="png" data-w="643" src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpEV3Ct0YPwBZEO1yZfibIRq3djrAeaIIVAZMeibhD7eqskxJF0kMqkbcw/640?wx_fmt=png"></figure><p data-tool="mdnice编辑器">修改底部标签:</p><pre data-tool="mdnice编辑器"><span></span><code>GSEAmultiGP(gsea_list = m_gsea_list,<br> geneSetID = <span>"GO:0002757"</span>,<br> exp_name = c(<span>"group1"</span>,<span>"group2"</span>,<span>"group3"</span>),<br> curve.col = ggsci::pal_d3()(<span>3</span>),<br> addPval = <span>T</span>,<br> pvalX = <span>0.99</span>,pvalY = <span>0.99</span>,<br> legend.position = <span>"right"</span>,<br> rect.bm.label = c(<span>"DOX"</span>,<span>"DMSO"</span>))<br></code></pre><figure data-tool="mdnice编辑器"><img data-ratio="0.7713841368584758" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpoLCcWxPxOic1IYQAMlnYZMW5KPqPBdicajiazTpYLE6UsEbdrEVuDDrSQ/640?wx_fmt=png" data-type="png" data-w="643" src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpoLCcWxPxOic1IYQAMlnYZMW5KPqPBdicajiazTpYLE6UsEbdrEVuDDrSQ/640?wx_fmt=png"></figure><blockquote data-tool="mdnice编辑器"><p><strong>这样就可以查看不同实验条件下通路的变化了。</strong></p></blockquote><h2 data-tool="mdnice编辑器"><span><span>4</span></span><span>结尾</span><span></span></h2><blockquote data-tool="mdnice编辑器"><p><strong>路漫漫其修远兮,吾将上下而求索。</strong></p></blockquote><hr data-tool="mdnice编辑器"><p data-tool="mdnice编辑器">欢迎加入生信交流群。加我微信我也拉你进 <strong>微信群聊</strong> <strong>老俊俊生信交流群</strong> <strong>(微信交流群需收取 20 元入群费用,一旦交费,拒不退还!(防止骗子和便于管理))</strong> 。QQ 群可免费加入, 记得进群按格式修改备注哦。</p><section data-tool="mdnice编辑器"><section><p><strong>老俊俊微信：</strong></p><figure><img data-ratio="1" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpER0jU9Z2jYzFkFFiaH2MbPBvnn383SmEjQkiaicT0ozZqzQQ8lpSMFK5A/640?wx_fmt=png" data-type="png" data-w="430" src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpER0jU9Z2jYzFkFFiaH2MbPBvnn383SmEjQkiaicT0ozZqzQQ8lpSMFK5A/640?wx_fmt=png"></figure><figure><img data-ratio="1.3668430335097002" data-src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpM2lI6mzYIU5je0NEfH493zqdw6WvvLdrel5IBiaZyjff2NTnHPkJVEw/640?wx_fmt=png" data-type="png" data-w="567" src="https://mmbiz.qpic.cn/sz_mmbiz_png/G5jjcE4useyib8cOmnJpicniaZUy78dYKicpM2lI6mzYIU5je0NEfH493zqdw6WvvLdrel5IBiaZyjff2NTnHPkJVEw/640?wx_fmt=png"></figure></section><section><p><strong>知识星球：</strong></p><figure><img data-ratio="1.5896226415094339" data-src="https://mmbiz.qpic.cn/sz_mmbiz_jpg/G5jjcE4useyib8cOmnJpicniaZUy78dYKicp2mt41j2hA06500QQzsBCTmele6eW0eZ7oPCia3aJq3LI2iaU7TYtzc1g/640?wx_fmt=jpeg" data-type="jpeg" data-w="1060" src="https://mmbiz.qpic.cn/sz_mmbiz_jpg/G5jjcE4useyib8cOmnJpicniaZUy78dYKicp2mt41j2hA06500QQzsBCTmele6eW0eZ7oPCia3aJq3LI2iaU7TYtzc1g/640?wx_fmt=jpeg"></figure></section></section><hr data-tool="mdnice编辑器"><p data-tool="mdnice编辑器"><br></p><center data-tool="mdnice编辑器"><strong> 往期回顾目录</strong></center><blockquote data-tool="mdnice编辑器"><p><br></p><center><strong><a href="https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509821&idx=1&sn=66d6b4c47efed6c8dbfd9f2027d5a015&chksm=c1849d4cf6f3145af6077e06c25e4b9f3b5c7f7b93bf5ca507e56d4dd74d399df896dbd8c5d5&token=778653154&lang=zh_CN&scene=21#wechat_redirect" data-linktype="2">grid 里绘制连续型图例</a></strong></center><strong><center><a href="https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509799&idx=1&sn=b3bc4bbbb8c1e3a98be3f5815cbcb4f0&chksm=c1849d56f6f3144000e22d4b9ebf989ad79349c450928c2a2346749b0187d857fca15d9e7183&token=613129250&lang=zh_CN&scene=21#wechat_redirect" data-linktype="2">听说你要绘制 scanpy 版的散点图?</a></center></strong><strong><center><a href="https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509762&idx=1&sn=97596153e141170c7c6af1dab29499ac&chksm=c1849d73f6f31465bbb6d78217ead9b402f3b5ade770e23f9f35904ae2856392c3f332ba8c23&token=613129250&lang=zh_CN&scene=21#wechat_redirect" data-linktype="2">听说你要手搓一个 grid.xaxis2/grid.yaxis2?</a></center></strong><strong><center><a href="https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509735&idx=1&sn=212e45f9e6c8cfd13bc943b6ac806dc2&chksm=c1849c96f6f31580624e0d4bab65b47d7b3e4cf7fc604881fb9c27a32249bd071dd1eae20d66&token=613129250&lang=zh_CN&scene=21#wechat_redirect" data-linktype="2">用 grid 手搓一个单细胞散点图+细胞数量条形图</a></center></strong><strong><center><a href="https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509673&idx=1&sn=d1459c0c3790d87902b296c4cceae60f&chksm=c1849cd8f6f315ce7d7249971e39900b72d8fd897e778873a1ac1b8b27f4bfdcfd54ab45dd1b&token=868587677&lang=zh_CN&scene=21#wechat_redirect" data-linktype="2">lattice 分面设置</a></center></strong><strong><center><a href="https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509656&idx=1&sn=184ada98f9f6601deac7b402a737032d&chksm=c1849ce9f6f315ffdcbb0c32d70a337648ee4c4715d9261ba946f0233456df09e79472214d15&token=942343261&lang=zh_CN&scene=21#wechat_redirect" data-linktype="2">获取字符串的长度和宽度</a></center></strong><strong><center><a href="https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509621&idx=1&sn=9bb204ed21066faf253bee488c194e02&chksm=c1849c04f6f31512470c3f315ca964120b93efe2868c1a490a1fd9aa211e7c6eaaf3d0cd647c&token=540433608&lang=zh_CN&scene=21#wechat_redirect" data-linktype="2">piggyback 轻松像向 github 上传大文件</a></center></strong><strong><center><a href="https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509603&idx=1&sn=6d41b84e829740f9e59fb76e2304db7e&chksm=c1849c12f6f31504ea91f974728195c3e008c898ed6c6c5c41b15786bfbe03b7c2eaf8cc90c3&token=7125559&lang=zh_CN&scene=21#wechat_redirect" data-linktype="2">ClusterGVis 添加 GSEA 富集图</a></center></strong><strong><center><a href="https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509592&idx=1&sn=ded92cd239b4d0d03b516750511a0161&chksm=c1849c29f6f3153f7e87c687ac24d0a1ec43c6a697ab7669baa011611cc8e4b7220fa110e6bb&token=7125559&lang=zh_CN&scene=21#wechat_redirect" data-linktype="2">使用 lattice 绘制散点图</a></center></strong><strong><center><a href="https://mp.weixin.qq.com/s?__biz=MzkyMTI1MTYxNA==&mid=2247509534&idx=1&sn=80ced13313c341ff5c3230d71f6e0fa7&chksm=c1849c6ff6f3157957031171f14dc698646a6a60872e1bb695c72fe19c86a9ed50d03a2ca74a&token=1097150266&lang=zh_CN&scene=21#wechat_redirect" data-linktype="2">ggh4x 部分实用功能分享</a></center></strong><p><br></p></blockquote></section><p><mp-style-type data-value="3"></mp-style-type></p></div> | ||
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