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- library(readr)
- library(stringr)
- library(ggplot2)
- library(ggseqlogo)
- setwd("~/Documents/NPS James/MEME sequence logo plots/Fig2/Search1")
- # Provide path to meme matrix files
- input <- list.files("~/Documents/NPS James/MEME sequence logo plots/Fig2/Search1")
- # Read files and prepare list for ggseqlogo
- Fig2A <- list()
- for (i in 1:length(input)) {
- x <- data.matrix(read.table(input[i],header = TRUE, sep = "", numerals = c("no.loss")), rownames.force = NA)
- x <- t(x)
- Fig2A[[i]]<-x
- }
- ggseqlogo(Fig2A, ncol=1)
- setwd("~/Documents/NPS James/MEME sequence logo plots/Fig2")
- # Save plot to pdf
- pdf('2A.pdf', width=6.5, height=5)
- ggseqlogo(Fig2A, ncol=1)
- dev.off()
- setwd("~/Documents/NPS James/MEME sequence logo plots/Fig2/Search2")
- input2 <- list.files("~/Documents/NPS James/MEME sequence logo plots/Fig2/Search2")
- Fig2B <- list()
- for (i in 1:length(input2)) {
- x <- data.matrix(read.table(input2[i],header = TRUE, sep = "", numerals = c("no.loss")), rownames.force = NA)
- x <- t(x)
- Fig2B[[i]]<-x
- }
- setwd("~/Documents/NPS James/MEME sequence logo plots/Fig2")
- pdf('2C.pdf', width=6.89, height=1.6)
- ggseqlogo(Fig2B, ncol=1)
- dev.off()
- setwd("~/Documents/NPS James/MEME sequence logo plots/Fig3")
- input3 <- list.files("~/Documents/NPS James/MEME sequence logo plots/Fig3")
- Fig3 <- list()
- for (i in 1:length(input3)) {
- x <- data.matrix(read.table(input3[i],header = TRUE, sep = "", numerals = c("no.loss")), rownames.force = NA)
- x <- t(x)
- Fig3[[i]]<-x
- }
- pdf('3.pdf', width=6.6, height=3.2)
- ggseqlogo(rev(Fig3), ncol=1)
- dev.off()
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