富集结果聚类展示：clusterProfiler/enrichplot/treeplot

这几张图都挺好看的，不放再展示通路的时候试试看！！！

library(clusterProfiler)
library(org.Hs.eg.db)
library(enrichplot)
library(GOSemSim)
library(ggplot2)
library(DOSE)
data(geneList)

gene <- names(geneList)[abs(geneList) > 2]
ego <- enrichGO(gene  = gene,
                universe      = names(geneList),
                OrgDb         = org.Hs.eg.db,
                ont           = "BP",
                pAdjustMethod = "BH",
                pvalueCutoff  = 0.01,
                qvalueCutoff  = 0.05,
                readable      = TRUE)
d <- godata('org.Hs.eg.db', ont="BP")
ego2 <- pairwise_termsim(ego, method = "Wang", semData = d)
treeplot(ego2, showCategory = 30)

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# use `hilight = FALSE` to remove ggtree::geom_hilight() layer.
treeplot(ego2, showCategory = 30, hilight = FALSE)

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# use `offset` parameter to adjust the distance of bar and tree.
treeplot(ego2, showCategory = 30, hilight = FALSE, offset = rel(1.5))

image.png

# use `offset_tiplab` parameter to adjust the distance of nodes and branches.
treeplot(ego2, showCategory = 30, hilight = FALSE, offset_tiplab = rel(1.5))

image.png

keep <- rownames(ego2@termsim)[c(1:10, 16:20)]
keep
treeplot(ego2, showCategory = keep)

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treeplot(ego2, showCategory = 20, 
         group_color = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442"))

image.png

# It can also graph compareClusterResult
data(gcSample)
xx <- compareCluster(gcSample, fun="enrichKEGG",
                     organism="hsa", pvalueCutoff=0.05)
xx <- pairwise_termsim(xx)                     
treeplot(xx)                     

image.png

# use `geneClusterPanel` to change the gene cluster panel.
treeplot(xx, geneClusterPanel = "dotplot")  

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treeplot(xx, geneClusterPanel = "pie")  

image.png