Plot TreeStructure tree with cluster and partition variables

Usage

# S3 method for class 'TreeStructure'
plot(x, use_ggtree = TRUE, ...)

Arguments

x: A TreeStructure object
use_ggtree: Toggle ggtree or ape plotting behaviour
...: Additional arguments passed to ggtree or ape::plot.phylo

Examples


tree <- ape::read.tree( system.file('sim.nwk', package = 'treestructure') )

(struc <- trestruct( tree ))
#> Tree has NA or duplicated tip labels. Adding a unique id.
#> Finding splits under nodes: 276 
#> Finding splits under nodes: 276 526 
#> Finding splits under nodes: 276 421 
#> Finding splits under nodes: 276 473 
#> Call: 

#> .trestruct(tre = tre, minCladeSize = minCladeSize, minOverlap = minOverlap, 
#>     nodeSupportValues = nodeSupportValues, nodeSupportThreshold = nodeSupportThreshold, 
#>     nsim = nsim, level = level[1], ncpu = ncpu, verbosity = verbosity, 
#>     debugLevel = debugLevel, useNodeSupport = useNodeSupport, 
#>     tredat = tredat)
#> 

#> Significance level: 0.01 
#> Number of clusters: 4 
#> Number of partitions: 2 
#> Number of taxa in each cluster:
#> 
#>   1   2   3   4 
#>  25  25 200  25 
#> Number of taxa in each partition:
#> 
#>   1   2 
#>  75 200 
#> ...

#> For complete data, use `as.data.frame(...)` 

#plot treestructure object

plot(struc)