NOTE: This software is no longer maintained.

Please use the new version of wiggleplotr available either from Bioconductor or GitHub.

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")

Usage

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.

Acknowledgements

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