Saturday, September 22, 2012

Fwd: ggbio: an R package for extending the grammar of graphics for genomic data

Fwd: please follow footer link
ggbio: an R package for extending the grammar of graphics for genomic data: We introduce ggbio, a new methodology to visualize and explore genomics annotations and high-throughput data. The plots provide detailed views of genomic regions, summary views of sequence alignments and splicing patterns, and genome-wide overviews with karyogram, circular and grand linear layouts. The methods leverage the statistical functionality available in R, the grammar of graphics and the data handling capabilities of the Bioconductor project. The plots are specified within a modular framework that enables users to construct plots in a systematic way, and are generated directly from Bioconductor data structures. The ggbio R package is available at http://tengfei.github.com/ggbio/.

## NOTES from the AUTHOR on his website


Thanks for your patience, you may notice that I have removed old documentations, I have to make it clear about documentation in next release(Oct 3rd).

I appologize you may end up with *endless loop* to find documentation, which bioconductor pdf vignette point to this website and this website point to bioconductor and so on. That's because in released version of ggbio(Bioc 2.10), we put every documentation in this website, which is hybrid of knitr+jekyll+github page. We are going to drop this style, because we document everything now in sweave or knitr, and would be part of bioconductor website for this package, it's more formal, so basically documentation of bioconductor packages will be better hosted on bioc website. Our principle would be keep one copy for those things(either source code or documentation) in one place.
ggplot2 0.9.2 is released on Sep.3rd, this will breaks tracks API in ggbio, I am working on solving this issue.
bioconductor 2.11 is going to be released on Oct 3rd(schedule), and I will put together all documentation and fixes and updates by then. By the time bioconductor is released, all vignettes with codes will be visible from bioconductor website. Before that time, I really appreciate your patience and attention for this package!


(Original Post: Genome Biology - Latest Articles.)