R语言绘制优雅的seqlogo图

参考代码

读取数据

data <- read.table(file = "WRKY.motif_prot.txt", header = F)
motifName <- c("MEME-1","MEME-2","MEME-3","MEME-4","MEME-5","MEME-6","MEME-7", "MEME-8","MEME-9", "MEME-10")

绘制单个seqlogo图

library(ggplot2)
library(ggseqlogo)

list <- c()
for (i in motifName) {
  seq <- as.character(data[data[,5] == i, 4])
  list[[i]] <- seq

  p<-ggplot() + geom_logo(seq) + theme_logo()

  pdf(paste(i, "seqlogo.pdf", sep = "."),width = 15 ,height = 5)
  print(p)
  dev.off()

  }

绘制整体seqlogo图

pdf(paste( "allmotif.seqlogo.pdf", sep = "."),width = 15 ,height = 50)
ggplot() + geom_logo(list) + theme_logo() +
  facet_wrap(~seq_group, ncol=1, scales='free_x')
dev.off()

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