Question: Creating Sequence Logos From The Command Line
6
gravatar for Qdjm
7.4 years ago by
Qdjm1.9k
Toronto
Qdjm1.9k wrote:

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.

visualization sequence motif • 4.1k views
ADD COMMENTlink modified 4.8 years ago by by0110 • written 7.4 years ago by Qdjm1.9k

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.

ADD REPLYlink written 7.4 years ago by Timtico330
7
gravatar for Jeremy Leipzig
7.4 years ago by
Philadelphia, PA
Jeremy Leipzig18k wrote:

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.

alt text

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Jeremy Leipzig18k
1

OK here it is: https://github.com/leipzig/berryLogo

ADD REPLYlink written 7.4 years ago by Jeremy Leipzig18k

That is a really neat way to present sequence logos!

ADD REPLYlink written 7.4 years ago by Gww2.6k

would be really interested to obtain the R code, did you have any luck with that?

ADD REPLYlink written 7.4 years ago by Timtico330

I agree with Timtico, this is cool, and I would like the code as well. We'll try it out. But not quite what I was looking for.

ADD REPLYlink written 7.4 years ago by Qdjm1.9k

i'll cook up some code that uses ggplot

ADD REPLYlink written 7.4 years ago by Jeremy Leipzig18k

thanks for that, i will try it out asap!

ADD REPLYlink written 7.4 years ago by Timtico330
5
gravatar for Timtico
7.4 years ago by
Timtico330
NL
Timtico330 wrote:

Use R and the packages seqLogo and Biostrings.

I used to use them to make perfect vectorised sequencelogos in PDF format.

ADD COMMENTlink written 7.4 years ago by Timtico330
2
gravatar for by0
4.8 years ago by
by0110
United Kingdom
by0110 wrote:

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

 

 

 

 

 

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by by0110
1
gravatar for Casey Bergman
7.4 years ago by
Casey Bergman17k
Athens, GA, USA
Casey Bergman17k wrote:

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.

ADD COMMENTlink written 7.4 years ago by Casey Bergman17k
1
gravatar for puthier
7.4 years ago by
puthier10
puthier10 wrote:

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.

http://rsat.ulb.ac.be/

ADD COMMENTlink written 7.4 years ago by puthier10
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