引言

❝
借助 circlize 把多个 GSEA 富集通路使用环形图进行展示，circGsea 函数封装在 GseaVis中。
安装

install.packages(“devtools”)

devtools::install_github(“junjunlab/GseaVis”)
使用示例

先富集分析：
library(ggplot2)
library(org.Hs.eg.db)
library(clusterProfiler)
library(dplyr)
library(GseaVis)

load test data

data(geneList, package=”DOSE”)

gse <- gseGO(geneList = geneList,
ont = “BP”,
keyType = “ENTREZID”,
OrgDb = org.Hs.eg.db)

gse <- setReadable(x = gse,OrgDb = org.Hs.eg.db,keyType = “ENTREZID”)

df_gse <- data.frame(gse)
geneSetID <- sample(df_gse$ID,size = 5)
然后拿这个对象来绘图：
circGsea(object = gse,
geneSetID = geneSetID)

修改通路形式：
circGsea(object = gse,
geneSetID = geneSetID,
GoIDfacing = “bending.inside”)

添加通路名称：
circGsea(object = gse,
geneSetID = geneSetID,
addDescription = T)

调整一下距离：
circGsea(object = gse,
geneSetID = geneSetID,
addDescription = T,
descripLength = 50,
descripShift = 1.5)

不弯曲显示：
circGsea(object = gse,
geneSetID = geneSetID,
addDescription = T,
descriptionFacing = “outside”,
descripShift = 1.5)

修改背景色：
circGsea(object = gse,
geneSetID = geneSetID,
bgCol = circlize::rand_color(n = 5))

修改热图颜色：
circGsea(object = gse,
geneSetID = geneSetID,
htCol = c(“#339933″,”#9933CC”))

修改曲线颜色：
circGsea(object = gse,
geneSetID = geneSetID,
htCol = c(“#339933″,”#9933CC”),
curveCol = “#003399”)

添加基因的排序，会比较慢一些：
circGsea(object = gse,
geneSetID = geneSetID,
addGeneRank = T)

换个显示样式：
circGsea(object = gse,
geneSetID = geneSetID,
type = “h”)

添加点：
circGsea(object = gse,
geneSetID = geneSetID,
type = “h”,
addPoints = T)

修改竖线的颜色：
circGsea(object = gse,
geneSetID = geneSetID,
type = “h”,
segmentsCol = “#003366”)

居中显示：
circGsea(object = gse,
geneSetID = geneSetID,
type = “m”)

标记一些基因：
mgene <- sample(gse@gene2Symbol,size = 3)

circGsea(object = gse,
geneSetID = geneSetID,
markGene = mgene)

结尾

❝
路漫漫其修远兮,吾将上下而求索。
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