I am using MATLAB to produce anything and everything. The question is not specific, yet if there is novelty in the field I would not want to miss out, Thank YOU
Edit:
So, I read this as: recommend your favourite visualization tool for bioinformatics/biological data, and link articles describing novel, ground-breaking visualization tools and methods. Still not a very specific question. Also, recommend introductory material/books so OP can read-up on the relevance of visualization techniques in bioinformatics and bio-statistics.
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Eminencegrise
4 answers
Assuming that you are not asking about anything specific, here are some interesting projects, in my opinion. The first is just a "gallery" but the second two are tools for creating plots.
http://addictedtor.free.fr/graphiques/
Those three can keep one busy for quite some time....
same - although ggplot2 syntax takes some getting used to
I'm writing this answer primarily because I think the ones already here are good, but in their scope misleading for users that find this question via Google (as I'm not sure which answer will help eminencegrise and he did not really elaborate on that so far).
The question really is what you are trying to do. There is no "one fits it all" plotting library, as there is generally no tool to do everything you would ever want it to. For instance, which programming language(s) do you want to use? Or rather have a (semi-)graphical interface for plotting? Do you want to have a ready-made graphic or be able to interact with it (zoom, etc.)?
So, I think the best approach would be to choose 1-3 languages you are comfortable with and then look for plotting libraries that are supported that fit your needs. We have already seen good answers for the R language (R native plotting which I think uses gnuplot -at least on Linux- and Bioconductor plotting, both simple, straightforward, and not very pretty, and ggplot, which is a "publication-quality" library).
There is also Octave plotting (very similar to Matlab) - also using gnuplot, thus not really supporting interaction with your data after visualization. Not using gnuplot, there is e.g. matplotlib, a very good library for the Python language. There are also some more ;-)
A lot of Biostar users might have very valuable input on this (which I myself would be interested in; e.g., I did not really know circos before, thank you to Shawn because now I do), but it is impossible to answer your question based on the information you provided.
yes, i know this should have been a comment and not an answer- it just was a little to long- don't feel obligated to vote it up
I am happy as foremost I was interested in what others people use and like as doing everything in Matlab makes life easier yet at times fresh ideas serve as great input for publication, Thank You
I agree fully with the sentiments in Michael's answer--there is no right answer here.
Just to clarify--R has many graphics devices that can be used, but it does not use gnuplot that I know of, even on linux. Also, "Bioconductor plotting" is, of course, just an application of R graphical tools.
Looking for a recent review paper related to visualization of high-throughput data? Here is one, maybe I add some more later:
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What's a biofigure? Do you mean statistical plots?
your question is not specific enough . Furthermore your already asked 10 questions on this site but didn't validated any of the answers (Close ?)
give him a day or 2 to edit first, this could potentially be of interest to others as well
yes indeed this is about statistical plots, I do realize this aint specific yet people tend to get used to certain tools, for me this is MATLAB yet I thought maybe someone is using other software to produce potent visualizations, thank YOU
Dear Pierre, what do You mean by validation?
He means that you did not accept any answers to your questions. You should click on the checkmark of the one which you think is the right one. Also, please edit your question to make clear what it's about instead of just writing clarifications in the comments.