ggseqlogo is an R package for generating publication-ready sequence logos using ggplot2.
Getting started
First install ggseqlogo from github using the devtools package:
devtools::install_github("omarwagih/ggseqlogo")Load up the package and sample data
# Load the required packages
require(ggplot2)
require(ggseqlogo)
# Some sample data
data(ggseqlogo_sample)
Then draw a sequence logo
# Plot DNA sequence logo for transcription factor - data from JASPAR
ggseqlogo( seqs_dna$MA0001.1 )
# Plot protein sequence logo for kinase target phosphosites
ggseqlogo( seqs_aa$AKT1 )For more examples, and a list of features see the full tutorial here.
Tutorial
A detailed tutorial on how to use ggseqlogo can be found here.
Citation
If you use ggseqlogo, please cite:
Wagih, Omar. ggseqlogo: a versatile R package for drawing sequence logos. Bioinformatics 33, no. 22 (2017): 3645-3647. https://doi.org/10.1093/bioinformatics/btx469 PMID: 29036507
Feedback
If you have any feedback or suggestions, drop me a line at (omarwagih(at)gmail.com) or open an issue on github.