Code to accompany https://seandavi.github.io/2019/05/single-cell-packages-and-dependencies-in-bioconductor-using-biocpkgtools/

single_cell_bioc_dependencies_with_biocpkgtools.R

# To accompany: https://seandavi.github.io/2019/05/single-cell-packages-and-dependencies-in-bioconductor-using-biocpkgtools/
library(BiocPkgTools)
library(igraph)
library(visNetwork)
bpl = biocPkgList()
bpl_sc = bpl[grepl('SingleCell', bpl$biocViews),]
dep_df = buildPkgDependencyDataFrame()
dep_graph = buildPkgDependencyIgraph(dep_df)
dep_graph_sc = inducedSubgraphByPkgs(dep_graph, bpl_sc$Package )
ledges <- data.frame(color = c("green", "lightblue", "red"),
                     label = c("Depends", "Suggests", "Imports"), arrows =c("from", "from", "from"))
visnet_data = toVisNetworkData(dep_graph_sc)
visnet_data$nodes$color=NULL
visNetwork(nodes = visnet_data$nodes, edges = visnet_data$edges, height = "500px") %>% 
  visNodes(size=50, font = list(size=50)) %>% 
  visIgraphLayout("layout_with_dh", weight.node.dist=15)