Return a minimal subgraph based on package name(s)

Find the subgraph induced by including specific packages. The induced subgraph is the graph that includes the named packages and all edges connecting them. This is useful for a developer, for example, to examine her packages and their intervening dependencies.

inducedSubgraphByPkgs(g, pkgs, pkg_color = "red")

Arguments

g

an igraph graph, typically created by buildPkgDependencyIgraph()

pkgs

character() vector of packages to include. Package names not included in the graph are ignored.

pkg_color

character(1) giving color of named packages. Other packages in the graph that fall in connecting paths will be colored as the igraph default.

Examples

library(igraph)
g <- buildPkgDependencyIgraph(buildPkgDependencyDataFrame())
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://cran.rstudio.com
## subgraph of only the first 10 packages maintained by Bioconductor
biocmaintained <- head(biocMaintained()[["Package"]], 10L)
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://cran.rstudio.com
g2 <- inducedSubgraphByPkgs(g, pkgs = biocmaintained)
g2
#> IGRAPH 7361c09 DN-- 10 11 -- 
#> + attr: name (v/c), color (v/c), edgetype (e/c)
#> + edges from 7361c09 (vertex names):
#>  [1] annotate         ->AnnotationDbi   annotate         ->Biobase        
#>  [3] AnnotationDbi    ->Biobase         AnnotationForge  ->AnnotationDbi  
#>  [5] AnnotationForge  ->Biobase         AnnotationHub    ->AnnotationDbi  
#>  [7] AnnotationHub    ->BiocVersion     AnnotationHubData->AnnotationDbi  
#>  [9] AnnotationHubData->AnnotationForge AnnotationHubData->AnnotationHub  
#> [11] AnnotationHubData->Biobase        
V(g2)
#> + 10/10 vertices, named, from 7361c09:
#>  [1] annotate          AnnotationDbi     AnnotationForge   AnnotationHub    
#>  [5] AnnotationHubData Biobase           AnnotationFilter  Bioc.gff         
#>  [9] BiocStyle         BiocVersion      

plot(g2)


## subgraph of a package's strong Bioconductor package dependencies
maedeps <- unlist(pkgBiocDeps(
    "MultiAssayExperiment", which = "strong",
    recursive = TRUE, only.bioc = TRUE
), use.names = FALSE)
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> 'help("repositories", package = "BiocManager")' for details.
#> Replacement repositories:
#>     CRAN: https://cran.rstudio.com
g3 <- inducedSubgraphByPkgs(g, pkgs = maedeps)
plot(g3)


## same subgraph with networkD3::forceNetwork
library(networkD3)
#> 
#> Attaching package: ‘networkD3’
#> The following object is masked from ‘package:htmlwidgets’:
#> 
#>     JS
wt <- cluster_walktrap(g3)
members <- membership(wt)
ndg3 <- igraph_to_networkD3(g3, group = members)
forceNetwork(
    Links = ndg3$links, Nodes = ndg3$nodes, Source = 'source',
    Target = 'target', NodeID = 'name', Group = 'group', zoom = TRUE,
    linkDistance = 200, fontSize = 20, opacity = 0.9, opacityNoHover = 0.9
)