getBiocSubViews: Build a list of BiocView objects from a package repository

In Bioconductor/biocViews: Categorized views of R package repositories

Build a list of BiocView objects from a package repository

Description

This function returns a list of BiocView-class objects corresponding to the subgraph of the views DAG induced by topTerm. In short, this does the same thing as getBiocViews, but limits the vocabulary to topTerm and all of its decendents.

Usage

getBiocSubViews(reposUrl, vocab, topTerm, local = FALSE, htmlDir = "")

Arguments

reposUrl	URL for a CRAN-style repository that hosts a VIEWS file at the top-level.
vocab	A graph-class object representing the ontologyof views. This graph should be a directed acyclic graph (DAG).
topTerm	A string giving the name of the subview DAG. This view and all of its decendents will be included in the result.
local	logical indicating whether to assume a local package repository. The default is FALSE in which case absolute links to package detail pages are created.
htmlDir	if the local argument is TRUE, this will be used as the relative path for package HTML files.

Details

The root of the vocabulary DAG is implicitly included in the view creation process order to build views with a link back to the top. It is removed from the return list.

This function is tailored to generation of Bioconductor Task Views. With the current vocabulary, it probably only makes sense to call it with topView set to one of "Software", "AnnotationData", or "ExperimentData". This is a hack to allow the biocViews code to manage HTML views across more than one repository.

Value

A list of BiocView-class objects. The names of the list give the name of the corresponding view.

Author(s)

Seth Falcon

See Also

write_VIEWS, writeBiocViews

Examples

data(biocViewsVocab)
reposPath <- system.file("doc", package="biocViews")
reposUrl <- paste("file://", reposPath, sep="")
biocViews <- getBiocSubViews(reposUrl, biocViewsVocab, "Software")
print(biocViews[1:2])

Bioconductor/biocViews documentation built on Nov. 2, 2024, 7:23 a.m.