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(This article was first published on <strong><a href="https://guangchuangyu.github.io/2017/08/joyplot-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>I am very glad to find that someone figure out <a rel="nofollow" href="https://stackoverflow.com/questions/45384281/ggjoy-facet-with-ggtree" target="_blank">how to use ggjoy with ggtree</a>.</p>
<p><img alt="" src="https://i1.wp.com/i.stack.imgur.com/U7D3j.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p>I really love ggjoy and believe it can be a good tool to visualize gene set enrichment (GSEA) result. DOSE/clusterProfiler support several visualization methods.</p>

<p><strong>running score:</strong></p>
<p><img alt="" src="https://i2.wp.com/guangchuangyu.github.io/blog_images/Bioconductor/clusterProfiler/mesh_gsea.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p><strong>enrichment map:</strong></p>
<p><img alt="" src="https://i1.wp.com/guangchuangyu.github.io/blog_images/Bioconductor/ReactomePA/c5mb00663e-f1_hi-res.gif?w=456&ssl=1" data-recalc-dims="1"></p>
<p><strong>category-gene-network:</strong></p>
<p><img alt="" src="https://i1.wp.com/guangchuangyu.github.io/blog_images/Bioconductor/clusterProfiler/2016_GO_analysis_using_clusterProfiler_files/figure-markdown_strict/unnamed-chunk-4-3.png?w=456&ssl=1" data-recalc-dims="1"></p>
<p><strong>dotplot:</strong></p>
<p><img alt="" src="https://i1.wp.com/guangchuangyu.github.io/blog_images/Bioconductor/DOSE/dotplot_geneRatio.png?w=456&ssl=1" data-recalc-dims="1"></p>
<hr>
<p>These visualization methods are designed for visualizing/summarizing enrichment results and none of them can incoporate expression values.</p>
<p>In DOSE v>=3.3.2, I defined a <code>joyplot</code> function, which can visualize GSEA result with expression distribution of the enriched categories.</p>
<p>Here is an example:</p>
<pre><code>require(clusterProfiler)
data(geneList)
x &lt;- gseKEGG(geneList)
joyplot(x)
</code></pre>
<p><img alt="" src="https://i2.wp.com/guangchuangyu.github.io/blog_images/Bioconductor/DOSE/joyplot_gsea.png?w=456&ssl=1" data-recalc-dims="1"></p>
	<p>
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