What's your favourite way to create sequence logos from the command line or programmatically?
This is in response to a question at StackOverflow on making sequence logos in ggplot2. I looked here and was surprised that couldn't find the answer.
Ideally, the package would be easy to use but flexible enough to show different logo representations (e.g. scale height by frequency or by information content) and different alphabets (DNA, RNA, and amino acids).
We have our own way of doing this in the lab, and being a PI, I don't know what it is, but I would like to hear other options.
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Qdjm
6 answers
There are some well-known problems with sequence logos, namely that the most frequent nucleotide gets top billing even if it is only a fraction more frequent than the runner-up.
Charles Berry developed an alternative that mitigates some of these issues.
An example is in this paper:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664696/
I can ask the programmer there to dig up the R code although it shouldn't be hard to replicate.
i'll cook up some code that uses ggplot
OK here it is: https://github.com/leipzig/berryLogo
Check out RWebLogo. It's an R wrapper for the WebLogo python library. It can be downloaded from CRAN: http://cran.r-project.org/web/packages/RWebLogo/index.html
and is hosted on github: https://github.com/omarwagih/RWebLogo
We have tried WebLogo and SeqLogo, but ultimately wrote our own routines in R for maximal flexibility in terms of layout of plots and figures.
I would suggest RSAT that can also be used as a stand-alone application and which implements lots of unix commands for position weight matrix analysis.
Try an independent implementation from the motif set to the Sequence logo, or a direct offline application here: Make a Sequence Logo in your browser by using native Javascript
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if you want i can provide the sourcecode of my way of doing it (see my answer). However it might be a bif different of our approach as I use Perl scripts to build position weight matrices.