## ----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 = ' '))