The new visualization package for genome data in Bioconductor: ggbio
It’s been a while since I’ve been waiting for the release of a visualization package in Bioconductor. Back in 2008 I was really impressed by the power of GenomeGraphs and I have used it in multiple occasions. Yet from both the Bioconductor Developer Meeting in Heidelberg 2010 and BioC2011 I’ve been waiting for the release of the visualization tools developed by Michael Lawrence and Tengfei Yin at Genentech.
So, after a long hiatus where I didn’t browse the biocviews in Bioconductor, I found out that Lawrence and Yin released ggbio and biovizBase (it’s more of an infrastructure package for ggbio) . I haven’t really had the time to play around with them, but it’s definitely worth exploring both of their vignette files: ggbio, biovizBase. I also think that they’ll fit very well in Bioconductor because quite a few of their examples involved the gamma of objects the BioC team has released for high-throughput sequencing (HTS) data. Meaning that they work well with objects from IRanges and GenomicRanges. Also, some of the examples use BAM files which are common nowadays in any HTS analysis pipeline. As a plus, ggbio uses ggplot2, which definitely makes clear nice plots.
I expect ggbio to replace GenomeGraphs soon (although I love using it), but I’m also kind of disappointed that I didn’t see any of the cool examples from BioC2011 in ggbio’s vignette file. After all, visnab looked pretty impressive as you can see in this presentation. I don’t know if they decided to rename visnab into ggbio, or maybe they haven’t released visnab yet. Anyhow, give ggbio and biovizBase vignette files a look :)