富集网络

收集一下目前富集分析能够形成网络图的现成的方式

FGNet

FGNet (bioconductor.org)

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("FGNet")

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cytoscape

Cytoscape Inroduction and Enrichment Map - YouTube

用网络图展示富集分析

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CBNplot

CBNplot: Bayesian network plots for enrichment analysis | Bioinformatics | Oxford Academic (oup.com)

Y叔手下出品

library(devtools)
install_github("noriakis/CBNplot")

文档
CBNplot (noriakis.github.io)

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clusterProler包

R tips：交互式网络图展示GO富集子通路 (tencent.com)

library(clusterProfiler)
# 差异基因
data(geneList, package="DOSE")
gene     <- names(geneList)[abs(geneList) > 2]

# 富集分析
ego <- enrichGO(gene          = gene,
                universe      = names(geneList),
                OrgDb         = org.Hs.eg.db,
                ont           = "CC",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.01,
                qvalueCutoff  = 0.05,
                readable      = TRUE)

# goplot
enrichplot::goplot(ego)

metascape 基因富集分析在线工具

Metascape

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当然还有其他方式，比如借助网络图自己写一个，具体怎么造，在五色绘图集前面的文章有一个方法