YuLab-SMU
关于gseaplot2的图例位置不能调节
Y叔您好，我最近在用clusterprofiler做GSEA时，发现gseaplot2绘制多个曲线图例会遮挡住曲线，我没找到可以调节图例位置的参数，想请教您这种情况该怎么办？
`library(clusterProfiler)
library(enrichplot)
library(DOSE)
library(data.table)
setwd("/Users/andrew/Desktop/COAD)/6 GSEA")
genelist_input=read.csv("edgerOut-order.csv",
header=TRUE,check.names = FALSE)
head(genelist_input)
geneList = genelist_input[,2]
names(geneList) = as.character(genelist_input[,1])
geneList = sort(geneList, decreasing = TRUE)
Go_gseresult_all <- gseGO(geneList, 'org.Hs.eg.db',
keyType = 'ENTREZID',
ont='BP',
nPerm = 1000,
minGSSize = 10,
maxGSSize = 1000,
pvalueCutoff=1)
Go_gseresult_all@result = Go_gseresult_all@result[order(Go_gseresult_all@result[,"NES"]),]
Go_gseresult_pNES = Go_gseresult_all
Go_gseresult_pNES@result <- subset(Go_gseresult_pNES@result, NES > 0)
Go_gseresult_pNES@result <- subset(Go_gseresult_pNES@result, pvalue < 0.05)
Go_gseresult_pNES@result = Go_gseresult_pNES@result[order(Go_gseresult_pNES@result[,"pvalue"]),]
Go_gseresult_nNES = Go_gseresult_all
Go_gseresult_nNES@result <- subset(Go_gseresult_nNES@result, NES < 0)
Go_gseresult_nNES@result <- subset(Go_gseresult_nNES@result, pvalue < 0.05)
Go_gseresult_nNES@result = Go_gseresult_nNES@result[rev(order(Go_gseresult_nNES@result[,"pvalue"])),]
Go_gseresult_recomb = Go_gseresult_pNES
Go_gseresult_recomb@result <- rbind(Go_gseresult_pNES@result, Go_gseresult_nNES@result)
nrow_Go_gseresult_recomb = as.numeric(nrow(Go_gseresult_recomb@result))
gseaplot2(Go_gseresult_recomb, c(1:3, c(nrow_Go_gseresult_recomb-2):nrow_Go_gseresult_recomb),
base_size = 15,
rel_heights = c(3, 1, 1),
subplots = 1:2,
ES_geom = "line",
pvalue_table = FALSE) #line or dot
write.csv(Go_gseresult_recomb@result, "Go_gseresult_recomb.csv")`
可以trace(gseaplot2, edit = TRUE)，去第26行修改legend.position，我改成了c(0.25, 0.3)将图例调整到了左下角
