Convert a phylo object to a dendrogram object

phylo_to_dendrogram(obj, log = FALSE)

Arguments

obj: A phylo object.
log: Whether the height of the phylogenetic tree should be log-transformed (log10(x + 1)).

Details

The motivation is that phylogenetic tree may contain polytomies, which means at a certain node, there are more than two children branches. Available tools that do the conversion only support binary trees.

The returned dendrogram object is not in its standard format which means it can not be properly drawn by the plot.dendrogram function. However, you can still apply dendextend::cutree to the returned dendrogram object with no problem and the dendrogram can be properly drawn with the ComplexHeatmap package.

Value

A dendrogram object.

Examples

require(ape)
#> Loading required package: ape
data(bird.families)
d = phylo_to_dendrogram(bird.families)

require(ComplexHeatmap)
#> Loading required package: ComplexHeatmap
#> ========================================
#> ComplexHeatmap version 2.18.0
#> Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
#> Github page: https://github.com/jokergoo/ComplexHeatmap
#> Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
#> 
#> If you use it in published research, please cite either one:
#> - Gu, Z. Complex Heatmap Visualization. iMeta 2022.
#> - Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
#>     genomic data. Bioinformatics 2016.
#> 
#> 
#> The new InteractiveComplexHeatmap package can directly export static 
#> complex heatmaps into an interactive Shiny app with zero effort. Have a try!
#> 
#> This message can be suppressed by:
#>   suppressPackageStartupMessages(library(ComplexHeatmap))
#> ========================================
grid.dendrogram(d, test = TRUE)