A common task in bioinformatics analysis is the visualization of data, in particular creating figures for manuscripts. I have found R to be incredibly powerful for this task. However, the figures created using many base plotting functions are somewhat 'plain' for publication purposes. This often necessitates additional modification and annotation in Illustrator, Inkscape, etc.
It seems that virtually anything is possible but I'm interested in recommendations for packages/libraries that will help me create richer figures entirely within R.
If you want some specific examples of issues that I have found challenging, these include things like:
- legend creation
- creation of multi-panel figures with custom margins
- addition of unusual 'symbols' to plots (e.g. greek letters, etc.)
- use of transparency
- more control of fonts
I realize this is a broad question but I am keen to learn about any tricks that will help me push my figures closer to publication quality in R and minimize manual post processing.
Similar question: http://biostar.stackexchange.com/questions/18164/how-to-draw-genome-features-along-chromosome
If you want other software or language environments too in addition to R, see the post: http://biostar.stackexchange.com/questions/18390/best-graphics-gallery-or-blogs-for-bioinformatics-use
good survey/question. It seems we all have the same ones ;-)