<p><div><div><div><div data-width="100" data-show-faces="false" data-send="true" data-layout="button_count" data-height="21" data-href="https://www.r-bloggers.com/dotplot-for-gsea-result/"></div></div><div></div></div><div></div></div>
<div>
(This article was first published on <strong><a href="https://guangchuangyu.github.io/2016/12/dotplot-for-gsea-result"> R on Guangchuang YU</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<p><img alt="" src="https://i0.wp.com/guangchuangyu.github.io/blog_images/Bioconductor/DOSE/gseaplot.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p>For GSEA analysis, we are familar with the above figure which shows the running enrichment score. But for most of the software, it lack of visualization method to summarize the whole enrichment result.</p>
<p>In <a target="_blank" rel="nofollow" href="https://guangchuangyu.github.io/DOSE">DOSE</a> (and related tools including <a target="_blank" rel="nofollow" href="https://guangchuangyu.github.io/clusterProfiler">clusterProfiler</a>, <a target="_blank" rel="nofollow" href="https://guangchuangyu.github.io/ReactomePA">ReactomePA</a> and <a target="_blank" rel="nofollow" href="https://guangchuangyu.github.io/meshes">meshes</a>), we provide <code>enrichMap</code> and <code>cnetplot</code> to summarize GSEA result.</p>
<p><img alt="" src="https://i2.wp.com/raw.githubusercontent.com/GuangchuangYu/DOSE/master/vignettes/figures/enrichMap_gseNCG.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p>Here is an example of using <code>enrichMap</code> which is good to visualize relationship among enriched gene sets.</p>
<p><img alt="" src="https://i2.wp.com/guangchuangyu.github.io/blog_images/Bioconductor/DOSE/cnetplot_up.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p><code>cnetplot</code> excel on visualizing relationship among gene sets and corresponding core genes.</p>
<p>Now <a target="_blank" rel="nofollow" href="https://guangchuangyu.github.io/DOSE">DOSE</a> support visualize GSEA result using <code>dotplot</code> which can visualize more enriched gene sets in one figure. This is a <a target="_blank" rel="nofollow" href="https://github.com/GuangchuangYu/DOSE/issues/20">feature request</a> from <a target="_blank" rel="nofollow" href="https://github.com/guidohooiveld">@guidohooiveld</a>.</p>
<p><code>dotplot</code> was previously implemented in <code>DOSE</code> to visualize hypergeometric test result. I modified it to support GSEA result.</p>
<p>Internally, <code>.sign</code> was reserved for the sign of <code>NES</code> (activated for NES > 0 and suppressed for NES &lt; 0). We can pass <code>split</code> parameter and then it will apply <code>showCategory</code> by splitting the results. The following example plot 30 activated and 30 suppressed enriched disease sets.</p>
<p><img alt="" src="https://i2.wp.com/cloud.githubusercontent.com/assets/626539/21432102/fe02fe6e-c8a4-11e6-9ddb-f4d952792ba3.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p>PS: <code>Count</code> is the number of core genes and <code>GeneRatio</code> is <code>Count/setSize</code>.</p>
<h2>Citation</h2>
<p><strong><em>G Yu</em></strong>, LG Wang, GR Yan, QY He. <a target="_blank" rel="nofollow" href="http://bioinformatics.oxfordjournals.org/content/31/4/608">DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis</a>. <strong><em>Bioinformatics</em></strong> 2015, 31(4):608-609.</p>
<p>
<div data-badge-popover="right" data-altmetric-id="2788597" data-badge-type="donut"></div>
<p>
<div>
<div>To <strong>leave a comment</strong> for the author, please follow the link and comment on their blog: <strong><a href="https://guangchuangyu.github.io/2016/12/dotplot-for-gsea-result"> R on Guangchuang YU</a></strong>.</div>
<hr>
<a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers.com</a> offers <strong><a rel="nofollow" href="https://feedburner.google.com/fb/a/mailverify?uri=RBloggers">daily e-mail updates</a></strong> about <a title="The R Project for Statistical Computing" rel="nofollow" href="https://www.r-project.org/">R</a> news and <a title="R tutorials" rel="nofollow" href="https://www.r-bloggers.com/search/tutorial">tutorials</a> on topics such as: <a title="Data science" rel="nofollow" href="https://www.r-bloggers.com/search/data%20science">Data science</a>, <a title="Big Data" rel="nofollow" href="https://www.r-bloggers.com/search/Big%20Data">Big Data, <a title="R jobs" rel="nofollow" href="https://www.r-users.com/">R jobs</a>, visualization (<a title="ggplot and ggplot2 tutorials" rel="nofollow" href="https://www.r-bloggers.com/search/ggplot2">ggplot2</a>, <a title="Boxplots using lattice and ggplot2 tutorials" rel="nofollow" href="https://www.r-bloggers.com/search/boxplot">Boxplots</a>, <a title="Maps and gis" rel="nofollow" href="https://www.r-bloggers.com/search/map">maps</a>, <a title="Animation in R" rel="nofollow" href="https://www.r-bloggers.com/search/animation">animation</a>), programming (<a title="RStudio IDE for R" rel="nofollow" href="https://www.r-bloggers.com/search/RStudio">RStudio</a>, <a title="Sweave and literate programming" rel="nofollow" href="https://www.r-bloggers.com/search/sweave">Sweave</a>, <a title="LaTeX in R" rel="nofollow" href="https://www.r-bloggers.com/search/LaTeX">LaTeX</a>, <a title="SQL and databases" rel="nofollow" href="https://www.r-bloggers.com/search/SQL">SQL</a>, <a title="Eclipse IDE for R" rel="nofollow" href="https://www.r-bloggers.com/search/eclipse">Eclipse</a>, <a title="git and github, Version Control System" rel="nofollow" href="https://www.r-bloggers.com/search/git">git</a>, <a title="Large data in R using Hadoop" rel="nofollow" href="https://www.r-bloggers.com/search/hadoop">hadoop</a>, <a title="Web Scraping of google, facebook, yahoo, twitter and more using R" rel="nofollow" href="https://www.r-bloggers.com/search/Web+Scraping">Web Scraping</a>) statistics (<a title="Regressions and ANOVA analysis tutorials" rel="nofollow" href="https://www.r-bloggers.com/search/regression">regression</a>, <a title="principal component analysis tutorial" rel="nofollow" href="https://www.r-bloggers.com/search/PCA">PCA</a>, <a title="Time series" rel="nofollow" href="https://www.r-bloggers.com/search/time+series">time series</a>, <a title="finance trading" rel="nofollow" href="https://www.r-bloggers.com/search/trading">trading</a>) and more...
<img height="1" alt="" width="1" src="http://feeds.feedburner.com/~r/RBloggers/~4/gqsbjTAHtbk"></a></div>