plot_rpm: Make relatively pretty bar plots of coverage in a genome.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Make relatively pretty bar plots of coverage in a genome.

Description

This was written for ribosome profiling coverage / gene. It should however, work for any data with little or no modification, it was also written when I was first learning R and when I look at it now I see a few obvious places which can use improvement.

Usage

plot_rpm(
  input,
  workdir = "images",
  output = "01.svg",
  name = "LmjF.01.0010",
  start = 1000,
  end = 2000,
  strand = 1,
  padding = 100
)

Arguments

input	Coverage / position filename.
workdir	Where to put the resulting images.
output	Output image filename.
name	Gene name to print at the bottom of the plot.
start	Relative to 0, where is the gene's start codon.
end	Relative to 0, where is the gene's stop codon.
strand	Is this on the + or - strand? (+1/-1)
padding	How much space to provide on the sides?

Value

coverage plot surrounging the ORF of interest

See Also

[ggplot2]

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.