enrichplot-让你们对clusterProfiler系列包无法自拔.doc

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1、enrichplot让你们对clusterProfiler系列包无法自拔先来一段搞笑的街头卖膏药的视频，大家可以娱乐一下再继续往下看，因为我接下来就是要卖Y叔版「膏药」！大家喜欢clusterProfiler，除了功能强大、支持广泛之外，我想还有一点必须是可视化，毕竟大家都是视觉动物，颜值即正义。然而这些都是我早期的代码，我其实一直想重新写，希望可以全部用gplot2来实现，方便后续维护、更好看、更强大。而这在我博士毕业后，终于找了个时间重写了一遍，并且也加入了部分新的图形，我把这些代码重新打包，已经在Bioconductor上，叫enrichplot。有了这个包

2、，你们更加对clusterProfiler系列包无法自拔，让其它的工具毫无颜色。Theenrichplotpackageimplementsseveralmethodsforenrichmentresultvisualizationtohelpinterpretation.Itsupportsbothhypergeometrictestandgenesetenrichmentanalysis.Bothofthemarewidelyusedtocharacterizepathway/functionrelationshipstoelucidatemolecularm

3、echanismsfromhigh-throughputgenomicdata.TheenrichplotpackagesupportsvisualizingenrichmentresultsobtainedfromDOSE(Yuetal.2015),clusterProfiler(Yuetal.2012),ReactomePA(YuandHe2016)andmeshes.InducedGODAGgraphGeneOntology(GO)isorganizedasadirectedacyclicgraph.Aninsighfulwayoflookingatther

4、esultsoftheanalysisistoinvestigatehowthesignificantGOtermsaredistributedovertheGOgraph.ThegoplotfunctionshowssubgraphinducedbymostsignificantGOterms.library(clusterProfiler)data(geneList,package='DOSE')deabs(geneList)>2]ego'org.Hs.eg.db',ont='BP',readable=TRUE)library(enrichplot)goplo

5、t(ego)BarplotBarplotisthemostwidelyusedmethodtovisualizeenrichedterms.Itdepictstheenrichmentscores(e.g.pvalues)andgenecountorratioasbarheightandcolor.barplot(ego,showCategory=20)DotplotDotplotissimilartobarplotwiththecapabilitytoencodeanotherscoreasdotsize.Bothbarplotanddotplotsupport

6、sfacettingtovisualizesub-ontologiessimultaneously.dotplot(ego,showCategory=30)go'org.Hs.eg.db',ont='all')dotplot(go,split='ONTOLOGY')+facet_grid(ONTOLOGY~.,scale='free')Gene-ConceptNetworkBoththebarplotanddotplotonlydisplayedmostsignificantenrichedterms,whileusersmaywanttoknowwhichgen

7、esareinvolvedinthesesignificantterms.Thecnetplotdepictsthelinkagesofgenesandbiologicalconcepts(e.g.GOtermsorKEGGpathways)asanetwork.##removeredundentGOtermsego2cnetplot(ego2,foldChange=geneList)cnetplot(ego2,foldChange=geneList,circular=TRUE,colorEdge=TRUE)UpSetPlotTheupsetplotisanalt

8、ernat