Loop for plotting multiple plots from multiple files and save in multiple pdfs in r

Question

I am interested to plot multiple plots from multiple text files (each with 3 columns) in r. For eg I have 6 text files where V1(1st column value) = 1

1_d_a1_s.txt  
1_d_a2_s.txt  
1_d_a3_s.txt  
1_d_b1_s.txt  
1_d_b3_s.txt  
1_d_b3_s.txt   

and similarly 6 files for V1 =2, V1=3,......until V1=10 so total I have 60 files. V2 (2nd column) and V3 (3rd column) have different ranges also.

I can plot from 1 dataset but how to make a loop script to generate for all 10 datasets (each with 6 files) and save in respective pdfs?

My data and script for 1 dataset is as follows. Please guide. Thanks!

# my data (1_d_a1_s.txt)
V1  V2  V3
1   122 1
1   123 1
1   124 1
1   132 2
1   133 2
1   134 3
1   140 3
1   141 2
1   142 2
1   143 4
1   144 2
1   145 10

# my data (2_d_a1_s.txt)
V1  V2  V3
2   127 1
2   128 1
2   132 2
2   133 3
2   134 3
2   140 3
2   145 2
2   142 2
2   143 4
2   144 2
2   157 8

# Rscript for plotting data from 1 dataset
library(reshape2)
1_a1 <- read.table("1_d_a1_s.txt", header=FALSE, sep ="\t")
1_a2 <- read.table("1_d_a2_s.txt", header=FALSE, sep ="\t")
1_a3 <- read.table("1_d_a3_s.txt", header=FALSE, sep ="\t")
1_b1 <- read.table("1_d_b1_s.txt", header=FALSE, sep ="\t")
1_b2 <- read.table("1_d_b2_s.txt", header=FALSE, sep ="\t")
1_b3 <- read.table("1_d_b3_s.txt", header=FALSE, sep ="\t")

1_a1_r <- rename(1_a1,c(V1="A", V2="B", V3="C"))
1_a2_r <- rename(1_a2,c(V1="A", V2="B", V3="C"))
1_a3_r <- rename(1_a3,c(V1="A", V2="B", V3="C"))
1_b1_r <- rename(1_b1,c(V1="A", V2="B", V3="C"))
1_b2_r <- rename(1_b2,c(V1="A", V2="B", V3="C"))
1_b3_r <- rename(1_b3,c(V1="A", V2="B", V3="C"))

pdf("1_d_s.pdf")        
plot(NULL, lwd=1, xlim=range(1_a1_r$B, 1_a2_r$B, 1_a3_r$B,1_b1_r$B, 1_b2_r$B, 1_b3_r$B), ylim=range(1_a1_r$C, 1_a2_r$C, 1_a3_r$C,1_b1_r$C, 1_b2_r$C, 1_b3_r$C), xlab="B", ylab = "C", main="1_d_s Plot", xaxt="n")
axis(1, at = seq(0, 2000, by = 100), las = 2)                           
lines(1_a1_r$B,1_a1_r$C, pch=1, col= 1, lwd=1)
lines(1_a2_r$B,1_a2_r$C, pch=2, col= 2, lwd=1)
lines(1_a3_r$B,1_a3_r$C, pch=3, col= 3, lwd=1)
lines(1_b1_r$B,1_b1_r$C, pch=4, col= 4, lwd=1)
lines(1_b2_r$B,1_b2_r$C, pch=5, col= 5, lwd=1)
lines(1_b3_r$B,1_b3_r$C, pch=6, col= 6, lwd=1)
legend("topright",c("a1","a2", "a3", "b1", "b2", "b3"),col=c(1, 2, 3, 4, 5, 6), lwd=1, cex=1.0, text.font=8)
dev.off()

Answer 1

Your example is kinda hard to reproduce, here is a general template which may help.

Essentially you put each group of files in one directory. Iterate over each directory and each file that lies within.

#getwd()
for(i in 1:10){
  dir.create(path = paste0('dir',i),)
  setwd(paste0('dir',i))
  for(j in 1:6){
    df <- data.frame(V1 = 1, V2 = 2, V3 = 3)
    write.table(df, file = paste0('file',j,'.txt')) 
  }
  setwd('..')
}


d <- list.dirs(path = getwd(), full.names = T)
d <- d[grepl(x = d,'dir')]

for(i in d){
  setwd(i)
  pdf('helloworld.pdf')
  plot(0, type = 'n', xlim = c(-10,10), ylim = c(-10,10))
  f <- list.files(i, pattern  = 'txt')
  for(j in f){
    df <- read.table(j)
    points(df[,1],df[,2])
  }
  dev.off()
  setwd('..')
}