## ---- echo = FALSE------------------------------------------------------------ knitr::opts_chunk$set( eval=FALSE ) ## ----setup, include=FALSE----------------------------------------------------- # knitr::opts_chunk$set(echo = TRUE) ## ----------------------------------------------------------------------------- # if(!"RCy3" %in% installed.packages()){ # install.packages("BiocManager") # BiocManager::install("RCy3") # } # library(RCy3) ## ----------------------------------------------------------------------------- # install.packages('ape') # install.packages('phytools') # install.packages('igraph') # library(ape) # library(phytools) # library(igraph) ## ----------------------------------------------------------------------------- # tree <- phytools::read.newick(system.file("extdata","phylotree.newick", package="RCy3")) # ig <- ape::as.igraph.phylo(tree, FALSE) # boolean for whether tree is rooted or not # ig <- set_edge_attr(ig,'distance', value=tree$edge.length) # set distances as edge attributes ## ----------------------------------------------------------------------------- # createNetworkFromIgraph(ig, title="phylotree", collection = "phylotree") ## ----------------------------------------------------------------------------- # layoutNetwork(paste('force-directed', # 'defaultEdgeWeight=3', # 'defaultSpringCoefficient=5E-5', # 'defaultSpringLength=80', # sep = ' ')) ## ----------------------------------------------------------------------------- # createColumnFilter('junctions', 'id', "^Node\\\\d+$", "REGEX") # junctions<-getSelectedNodes() # setNodeWidthBypass(junctions,1) # setNodeHeightBypass(junctions,1) # setNodeLabelBypass(junctions, "") ## ----------------------------------------------------------------------------- # setEdgeLabelMapping('distance') ## ----------------------------------------------------------------------------- # layoutNetwork(paste('force-directed', # 'edgeAttribute="distance"', # 'type="1 - normalized value"', # 'defaultSpringCoefficient=5E-4', # 'defaultSpringLength=50', # sep = ' '))