# #——初始化,包括= FALSE ------------------------------------------------------ 库(knitr) opts_chunk美元集(警告= FALSE,消息= FALSE,缓存= FALSE) # #——风格,呼应= FALSE,结果= ' asis '------------------------------------ BiocStyle:减价 () ## ----------------------------------------------------------------------------- 库(BiocPkgTools)头(biocBuildReport ()) ## ---- eval = FALSE --------------------------------------------------------------- # problemPage (authorPattern = " v *凯里 ") ## ---- eval = FALSE --------------------------------------------------------------- # problemPage(取决于=“limma”)# #----------------------------------------------------------------------------- 头(biocDownloadStats ()) ## ----------------------------------------------------------------------------- 头(anacondaDownloadStats ()) ## ----------------------------------------------------------------------------- bpi = biocPkgList () colnames (bpi ) ## ----------------------------------------------------------------------------- 头(bpi) # #----------------------------------------------------------------------------- 要求(dplyr) bpi = biocPkgList () bpi % > %过滤器(包= =“GEOquery”)% > %拉(importsMe) % > % unlist () ## ---- biocExplore -------------------------------------------------------------- biocExplore () ## ----------------------------------------------------------------------------- 库(BiocPkgTools) dep_df = buildPkgDependencyDataFrame () g = buildPkgDependencyIgraph (dep_df) g库(igraph)头(V (g))头(E (g)) # #----------------------------------------------------------------------------- igraph_network = buildPkgDependencyIgraph (buildPkgDependencyDataFrame ()) ## ----------------------------------------------------------------------------- igraph_geoquery_network = subgraphByDegree (igraph_network,“GEOquery ") ## ----------------------------------------------------------------------------- 库(visNetwork)数据< - toVisNetworkData (igraph_geoquery_network ) ## ----------------------------------------------------------------------------- visNetwork(边缘节点=数据节点,美元=美元数据边缘,身高= " 500 px ") ## ----------------------------------------------------------------------------- visNetwork(边缘节点=数据节点,美元=数据边缘,美元身高= 500 px) % > % visPhysics(稳定= FALSE ) ## ----------------------------------------------------------------------------- 数据边缘颜色=“lightblue”美元美元边缘(数据边缘edgetype美元= =‘进口’,'颜色']=“红色”数据边缘美元[数据边缘edgetype美元= =“取决于”,'颜色']=“绿色”visNetwork(边缘节点=数据节点,美元美元=数据边缘,身高= 500 px) % > % visEdges(箭头= ' ') ## ----------------------------------------------------------------------------- 岩架< - data.frame(颜色= c(“绿色”,"浅蓝色"，"红色")，label =c("依赖"，"建议"，"导入")，箭头=c("from"， "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，宽度=“100%”)% > % visIgraphLayout(布局=“layout_as_tree”,圆= TRUE) % > % visNodes(大小= 20)% > % visPhysics(稳定= FALSE ) ## ----------------------------------------------------------------------------- 库(BiocPkgTools) depdf < - buildPkgDependencyDataFrame(回购= c(“BioCsoft”、“凹口”),依赖= c(“取决于”、“进口”))暗(depdf)头(depdf) #大到显示所有 ## ----------------------------------------------------------------------------- pkgDepMetrics(“BiocPkgTools”,depdf ) ## ----------------------------------------------------------------------------- 小鬼< - pkgDepImports (BiocPkgTools) imp % > %过滤器(pkg = =”DT ") ## ---- demoorc ------------------------------------------------------------------ 本月= rownames (installed.packages())萤石= c(“devtools”、“评价”、“ggplot2”、“GEOquery”,“哥特”、“跑龙套”)尝试=相交(萤石, inst) oids = get_cre_orcids(totry) oids ## ----lktab,eval=FALSE--------------------------------------------------------- # orcid_table(oids) ## ----------------------------------------------------------------------------- sessionInfo()