R package for Enrichment Depletion Logos (EDLogos) and String Logos
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README.md

Logolas

Logolas is an R package for Enrichment Depletion Logo plots with string symbols, including adaptive scaling of position-weight matrices (PWMs). Logolas can be considered an extension to the seqLogo package.

If you find a bug, please create an issue.

This code has been tested in ...

misc

License

Copyright (c) 2017-2018, Kushal Dey.

All source code and software in this repository are made available under the terms of the GNU General Public License. See the LICENSE file for the full text of the license.

Citing this work

If you find that this R package is useful for your work, please cite our paper:

Dey, K.K., Xie, D. and Stephens, M., 2017. A new sequence logo plot to highlight enrichment and depletion. bioRxiv doi:10.1101/226597.

Quick Start

The most recent version of Logolas available on Bioconductor can be easily installed by running these two commands in R:

source("https://bioconductor.org/biocLite.R")
biocLite("Logolas")

These commands will also install several other packages from CRAN and Bioconductor that are needed to run Logolas.

Alternatively, you can to install the most up-to-date development version. The easiest way to accomplish this is using the devtools package, but you will need to first install several packages from Bioconductor:

source("https://bioconductor.org/biocLite.R")
biocLite(c("Biostrings","BiocStyle","Biobase","seqLogo","ggseqlogo"))
library(devtools)
install_github("kkdey/Logolas",build_vignettes = TRUE)

Once you have installed the package, load the package in R by entering

library(Logolas)

To get an overview of the package, enter

help(package = "Logolas")

Next, try creating a few plots using the logomaker function:

sequence <- c("CTATTGT","CTCTTAT","CTATTAA","CTATTTA", "CTATTAT","CTTGAAT",
              "CTTAGAT","CTATTAA","CTATTTA","CTATTAT", "CTTTTAT","CTATAGT",
              "CTATTTT","CTTATAT","CTATATT","CTCATTT", "CTTATTT","CAATAGT",
              "CATTTGA","CTCTTAT","CTATTAT","CTTTTAT", "CTATAAT","CTTAGGT",
              "CTATTGT","CTCATGT","CTATAGT", "CTCGTTA","CTAGAAT","CAATGGT")
logomaker(sequence,type = "Logo")

misc

logomaker(sequence, type = "EDLogo")

misc

data(mutation_sig)
logomaker(mutation_sig, type = "EDLogo", color_type = "per_symbol",  color_seed = 2300)

misc

data(histone_marks)
logomaker(histone_marks$mat, bg = histone_marks$bgmat, type = "EDLogo")

misc

Finally, please walk through some more detailed examples in the vignette:

vignette("Logolas")

Developer notes

This was the R command used to generate the vignette PDF file from the R Markdown source:

render("Logolas.Rmd",output_format="pdf_document")

Credits

This software was developed by Kushal Dey Dongyue Xie and Matthew Stephens at the University of Chicago. For any questions or comments, please contact Kushal Dey at kkdey@uchicago.edu.

The authors would like to acknowledge Oliver Bembom, the author of the seqLogo fpackage or acting as an inspiration and giving us the base through his awesome package, on which we developed this software. The authors also thank Peter Carbonetto, Edward Wallace and John Blischak for helpful discussions and feedback.