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()