## ----init, include=FALSE------------------------------------------------------ library(knitr) opts_chunk$set(warning = FALSE, message = FALSE, cache=FALSE) ## ----style, echo = FALSE, results = 'asis'------------------------------------ BiocStyle::markdown() ## ----------------------------------------------------------------------------- library(BiocPkgTools) head(biocBuildReport()) ## ----eval=FALSE--------------------------------------------------------------- # problemPage(authorPattern = "V.*Carey") ## ----eval=FALSE--------------------------------------------------------------- # problemPage(dependsOn = "limma") ## ----------------------------------------------------------------------------- head(biocDownloadStats()) ## ----------------------------------------------------------------------------- head(anacondaDownloadStats()) ## ----------------------------------------------------------------------------- bpi = biocPkgList() colnames(bpi) ## ----------------------------------------------------------------------------- head(bpi) ## ----------------------------------------------------------------------------- require(dplyr) bpi = biocPkgList() bpi %>% filter(Package=="GEOquery") %>% pull(importsMe) %>% unlist() ## ----biocExplore-------------------------------------------------------------- biocExplore() ## ----------------------------------------------------------------------------- library(BiocPkgTools) dep_df = buildPkgDependencyDataFrame() g = buildPkgDependencyIgraph(dep_df) g library(igraph) head(V(g)) head(E(g)) ## ----------------------------------------------------------------------------- igraph_network = buildPkgDependencyIgraph(buildPkgDependencyDataFrame()) ## ----------------------------------------------------------------------------- igraph_geoquery_network = subgraphByDegree(igraph_network, "GEOquery") ## ----------------------------------------------------------------------------- library(visNetwork) data <- toVisNetworkData(igraph_geoquery_network) ## ----------------------------------------------------------------------------- visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") ## ----------------------------------------------------------------------------- visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>% visPhysics(stabilization=FALSE) ## ----------------------------------------------------------------------------- data$edges$color='lightblue' data$edges[data$edges$edgetype=='Imports','color']= 'red' data$edges[data$edges$edgetype=='Depends','color']= 'green' visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>% visEdges(arrows='from') ## ----------------------------------------------------------------------------- ledges <- data.frame(color = c("green", "lightblue", "red"), label = c("Depends", "Suggests", "Imports"), arrows =c("from", "from", "from")) visNetwork(nodes = data$nodes, edges = data$edges, height = "500px") %>% visEdges(arrows='from') %>% visLegend(addEdges=ledges) ## ----biocViews---------------------------------------------------------------- library(biocViews) data(biocViewsVocab) biocViewsVocab library(igraph) g = igraph.from.graphNEL(biocViewsVocab) library(visNetwork) gv = toVisNetworkData(g) visNetwork(gv$nodes, gv$edges, width="100%") %>% visIgraphLayout(layout = "layout_as_tree", circular=TRUE) %>% visNodes(size=20) %>% visPhysics(stabilization=FALSE) ## ----------------------------------------------------------------------------- library(BiocPkgTools) depdf <- buildPkgDependencyDataFrame(repo=c("BioCsoft", "CRAN"), dependencies=c("Depends", "Imports")) depdf ## ----------------------------------------------------------------------------- pkgDepMetrics("BiocPkgTools", depdf) ## ----------------------------------------------------------------------------- imp <- pkgDepImports("BiocPkgTools") imp %>% filter(pkg == "DT") ## ----------------------------------------------------------------------------- sessionInfo()