The aim of this project is to provide an interactive and convenient approach to visualize track-based genomic data in R, that is, to provide a simple genome browser within R environment to view objects in bioconductor like GRanges, GRangesList, TxDb, EnsDb.
Take a look at the package vignette!
The project is mentored by Toby Hocking and Miguel Pignatelli, under the organization of R project for statistical computing.
With the GSoC program, a new R package called TnT is successfully developed.
- The source repository is https://github.com/marlin-na/TnT .
- The package vignette can be found at https://marlin-na.github.io/TnT/articles/introduction.html .
- Some additional examples can be found at https://marlin-na.github.io/TnT/articles/examples .
- The project link at Google can be found at https://summerofcode.withgoogle.com/projects/#5521605556961280 .
Why called TnT?
TnT stands for 2,4,6-trinitrotoluene, which is best known as an explosive material.
About the start
In the beginning the Universe was created. This has made a lot of people very angry and been widely regarded as a bad move.
Meanwhile, I have been long heared of GSoC program through some blog posts and I would be more than excited to put this project idea into. But I need to find mentors. The R project in GSoC is quite easy to get started or get involved with. I wrote the wiki page and posted my idea in mailing list, and later asked Miguel as Toby suggested, then Toby and Miguel kindly take the mentorship for this project.
About the progress
I utilized the GRanges class from GenomicRanges package to store the track data and implemented constructors of tracks and methods to render tracks.
One problem I was initially worried about is that gene track and transcript track in TnT do not have public documentation to work with custom data source, but Miguel provided very nice examples and explanations on it, which thus solves the problem.
One original goal proposed for the project is to use headless browser testing to test the package, as suggested by Toby. Unfortunately this goal was not accomplished in the end. On the on hand, unlike other htmlwidget R packages, most parts of TnT are implemented on R side, on the other hand, I did not left enough time at the end and I tried to focus more on changes of the internal functions.
Overall, I enjoyed very much with this experience, and with help of my mentors, we have accomplished the main goal proposed for the project and overcomes problems in the way.
About the future
Currently in my mind, there are still several improvements that can and should be made for the package, including the direct support of EnsDb for gene and transcript tracks, alternative constructors of line track and area track from coverage, etc. But these changes are not likely to break the current api, and I will do them in the next future.
About my mentors
I would greatly thank my two mentors, Toby Hocking and Miguel Pignatelli, for their kind mentorship.
Toby Hocking has been the co-administrator and mentor for the R project in GSoC since 2012 and is an expert in data visualization and machine learning. He offered valuable instructions and kindly agreed to mentor this project when I approached to R project in GSoC with the porject idea, and then provided great instructions and feedback throughout the project.
Also thanks Google for providing such a great opportunity for students worldwide!
I am now a year-4 undergraduate student studying biological sciences, and looking for post-graduate studies in the field of bioinformatics or biostatistics. R is current my primary programming language and I love it.
Any comments about the project or the package would be appreciated!