GseaVis 多条通路可视化 - junjunlab/GseaVis GitHub Wiki

引言

Y 叔的 gseaplot2 可以可视化多条通路,但是 GseaVis 只能可视化单条通路的,有小伙伴也想让 GseaVis 来可视化多条通路,于是花了一些时间改了改代码,仿照着 gseaplot2 的样子画画。

安装

github 地址:

https://github.com/junjunlab/GseaVis

重新安装获取新功能:

# install.packages("devtools")
devtools::install_github("junjunlab/GseaVis")

欢迎大家在 github 上留下你的小心心。

测试

加载测试数据:

library(GseaVis)

# load data
test_data <- system.file("extdata", "gseaRes.RDS", package = "GseaVis")
gseaRes <- readRDS(test_data)

选择多条通路绘图:

geneSetID = c('GOBP_NUCLEOSIDE_DIPHOSPHATE_METABOLIC_PROCESS',
              'GOBP_REGULATION_OF_OSSIFICATION',
              'GOBP_TISSUE_MIGRATION')

# all plot
gseaNb(object = gseaRes,
       geneSetID = geneSetID)

保留上面两个图层:

# sub plot
gseaNb(object = gseaRes,
       geneSetID = geneSetID,
       subPlot = 2)

当然你也可以去除热图:

# remove heatbar
gseaNb(object = gseaRes,
       geneSetID = geneSetID,
       subPlot = 2,
       rmHt = T)

调整图例位置和长度:

# wrap term name and adjust position
gseaNb(object = gseaRes,
       geneSetID = geneSetID,
       subPlot = 2,
       termWidth = 35,
       legend.position = c(0.8,0.8))

当然你还可以标注通路里的基因名称:

# add gene name
gene <- c("Entpd8","Htr2a","Nt5e","Actn3","Entpd1",
          "Pfkp", "Tpi1","Igf1","Ddit4","Ak9")

gseaNb(object = gseaRes,
       geneSetID = geneSetID,
       subPlot = 2,
       termWidth = 35,
       legend.position = c(0.8,0.8),
       addGene = gene)

你还可以添加NES和P值,不过我这里 采用了表格的形式:

# add NES and Pvalue
gseaNb(object = gseaRes,
       geneSetID = geneSetID,
       subPlot = 2,
       termWidth = 35,
       legend.position = c(0.8,0.8),
       addGene = gene,
       addPval = T,
       pvalX = 0.05,pvalY = 0.05)

修改线条颜色, 如果超过四个通路,你可能得自己提供颜色,因为默认只有三个颜色:

# change line color
gseaNb(object = gseaRes,
       geneSetID = geneSetID,
       subPlot = 2,
       termWidth = 35,
       legend.position = c(0.8,0.8),
       addGene = gene,
       addPval = T,
       pvalX = 0.05,pvalY = 0.05,
       curveCol = jjAnno::useMyCol('paired',3))

结尾

感兴趣的小伙伴可以试试。有任何问题或者疑问欢迎在 github 留言讨论。