https://omarwagih.github.io/ggseqlogo/
Publication-quality sequence logos in R
https://omarwagih.github.io/ggseqlogo/
Last synced: 6 months ago
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Publication-quality sequence logos in R
- Host: GitHub
- URL: https://omarwagih.github.io/ggseqlogo/
- Owner: omarwagih
- Created: 2017-02-18T21:49:26.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-10-13T15:48:53.000Z (about 1 year ago)
- Last Synced: 2024-10-28T16:59:59.811Z (12 months ago)
- Language: R
- Homepage:
- Size: 10.8 MB
- Stars: 202
- Watchers: 13
- Forks: 30
- Open Issues: 24
-
Metadata Files:
- Readme: README.md
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README
[](http://cran.rstudio.com/web/packages/ggseqlogo/index.html)
[](http://cran.rstudio.com/web/packages/ggseqlogo/index.html)
ggseqlogo is an R package for generating publication-ready sequence logos using ggplot2.
## Getting started
First install `ggseqlogo` from github using the `devtools` package:
```r
devtools::install_github("omarwagih/ggseqlogo")
```
Load up the package and sample data
```r
# Load the required packages
require(ggplot2)
require(ggseqlogo)
# Some sample data
data(ggseqlogo_sample)
```
Then draw a sequence logo
```r
# 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](http://omarwagih.github.io/ggseqlogo/)**.
## Tutorial
A detailed tutorial on how to use ggseqlogo **[can be found here](http://omarwagih.github.io/ggseqlogo/)**.
## 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](https://doi.org/10.1093/bioinformatics/btx469) PMID: [29036507](https://www.ncbi.nlm.nih.gov/pubmed/29036507)
## Feedback
If you have any feedback or suggestions, drop me a line at (omarwagih(at)gmail.com) or open an issue on github.