Plotting a boxplot using R - r

Question

I am trying to create boxplot using R script from the following type of tab delimited file "New.txt" where the number of rows and columns will be variable
Chr Start End Name 18NGS31 18MPD168 18NGS21 18NGS29 18NGS33 18NGS38
chr9 1234 1234 ABL1 1431 1 1112 1082 1809 1647
chr9 2345 2345 ASXL1 3885 37 3578 1974 2921 3559
chr9 3456 3456 ETV6 3235 188 2911 1578 2344 2673
chr9 4567 4567 MYD88 3198 187 2860 1547 2289 2621
After skipping first four columns create box plot in R from 5th column on wards using following commands
file <- "new.txt"
x=read.table(file,skip=1)
boxplot(x$V5,x$V6,x$V7,x$V9,x$V10,x$V11,col=rainbow(54),xlab="abc",ylab="Coverage",main="Coverage Metrics")
And I am getting following box plot
[![R ploy][1]][1]
I want to modify this command such that I can incorporate any number of columns that will be present in the tab delimited file and label each box plot as per its column head.

Answer 1

I recommend reshaping from wide to long .
Here is a minimal example using ggplot2
# Sample data
df <- data.frame(id = paste0("id", 1:100), matrix(rnorm(1000), ncol = 10))
library(dplyr)
library(tidyr)
library(ggplot2)
df %>%
gather(key, value, -id) %>%
mutate(key = factor(key, levels = paste0("X", 1:10))) %>%
ggplot(aes(x = key, y = value)) +
geom_boxplot()
Explanation: Reshaping from wide to long stores the column names in a new column key and its values in value; we can then simply map key to x. This works for an arbitrary number of columns.
Update
Using your sample data
df <- read.table(text =
"Chr Start End Name 18NGS31 18MPD168 18NGS21 18NGS29 18NGS33 18NGS38
chr9 1234 1234 ABL1 1431 1 1112 1082 1809 1647
chr9 2345 2345 ASXL1 3885 37 3578 1974 2921 3559
chr9 3456 3456 ETV6 3235 188 2911 1578 2344 2673
chr9 4567 4567 MYD88 3198 187 2860 1547 2289 2621", header = T)
df %>%
gather(key, value, -Chr, -Start, -End, -Name) %>%
ggplot(aes(x = key, y = value, fill = key)) +
geom_boxplot()