WigglePlotR

A tool to create wiggle plots from RNA-Seq data.

Installation

Download the WigglePlotR.R file, start R and then run:

source("WigglePlotR.R")

You first have to import a bedfile using the following command:

bedfile <- ReadBedFile("path_to_bed_file.txt")

Then you can create a wiggle plot by running:

WigglePlotR(ids, bamfiles, bedfile, total.reads=NULL, cex = 1, kernel.width = 0
	exon.colors="black", intron.color="lightgray", exon.events = TRUE)

ids [character vector] -- IDs of the transcripts. Each ID must be present in the bedfile.
bamfiles [charcter vector] -- Full path to each BAM file containing the aligned reads.
bedfile [data.frame] -- BED file imported with ReadBedFile(). Specifies the structure of transcripts.
total.reads [numeric vector] -- Optional, total number of in each BAM file. When specified, used to normalize the y-axis to RPKM values.
cex [number] -- Scaling factor for text and axes. Default is cex = 1
kernel.width [number] -- Width of the kernel used to smoothen the wiggle plots. Default value is kernel.width = 1 which means no smoothing.
exon.colors [character vector] -- Color(s) for the reads overlapping exons.
intron.colors [character vector] -- Color(s) for the reads overlapping introns.
exon.events [boolean] -- If TRUE, first two transcripts will be colored differently from others and unique exons will be colored red.

This script is based on the the wiggleplots.R script originally written by Adam Gower.