Uml Diagram Of Bioconductor

Question

[Jamie]

Hi, Does anyone know whether a UML model of some core Bioconductor packages has been done? It would be good to see a visual representation of the relations between the different packages and their classes. TIA.

[User 59]

I admire your faith that UML is at some point deployed in the creation of an R package.

[Jamie]

@DanielSwan: not a very helpful comment. I never said I had faith that UML was deployed: I was asking whether it had been deployed. The development of Bioconductor was characterized by an adoption of an OOP paradigm. As such, it's not unreasonable to suggest that UML was used during development.

[Manu Prestat]

This is a good idea. Did you ask the R-help list ?

[Jamie]

No... to which R-help list are you referring? I have emailed the Bioconductor team but have yet to receive a response.

[User 59]

It was intended to be humorous and convey the likely result of your inquiry ;)

[Jamie]

Ok no problem..

Answer 1

[Sean Davis]

Give this a try:

source('http://bioconductor.org/biocLite.R')
biocLite('pkgDepTools')
library(pkgDepTools)
# grab the bioconductor repository url
repos = biocinstallRepos()[1]
# from the pkgDepTools package
z = makeDepGraph(repos)

Now, z is a graphNEL graph with nodes representing packages and directed edges from the package to its dependencies.

z
nodes(z)
edges(z)

You can use Rgraphviz to make a graphic of the dependencies or convert to igraph format for an interactive view. I leave that as an exercise.

As for classes, I don't have a good general answer for all classes, but for a specific class, the class definition will show you the relationships to classes from which the class inherits.

[Jamie]

Thanks, that's great. I've used graphviz before so I'll give it a try.

Answer 2

[Jamie]

I've received a reply saying that UML was not used in development of Bioconductor, but could be used to do model packages. I'll probably give it a try, unless someone's already done so?