circos.dendrogram: Add circular dendrograms

In eilslabs/circlize: Circular Visualization

Description

Add circular dendrograms

Usage

circos.dendrogram(dend, facing = c("outside", "inside"), max_height = NULL)

Arguments

dend	A dendrogram object.
facing	Is the dendromgrams facing inside to the circle or outside.
max_height	Maximum height of the dendrogram. This is important if more than one dendrograms are drawn in one track and making them comparable.

Details

Assuming there are n nodes in the dendrogram, the positions for leaves on x-axis is 0.5, 1.5, ..., n - 0.5. So you must be careful with xlim when you initialize the cirular layout.

You can use the dendextend package to render the dendrograms.

Examples

load(system.file(package = "circlize", "extdata", "bird.orders.RData"))

labels = hc$labels  # name of birds
ct = cutree(hc, 6)  # cut tree into 6 pieces
n = length(labels)  # number of bird species
dend = as.dendrogram(hc)

circos.par(cell.padding = c(0, 0, 0, 0))
circos.initialize(factors = "a", xlim = c(0, n)) # only one sector
max_height = attr(dend, "height")  # maximum height of the trees
circos.trackPlotRegion(ylim = c(0, 1), bg.border = NA, track.height = 0.3, 
    panel.fun = function(x, y) {
        for(i in seq_len(n)) {
            circos.text(i-0.5, 0, labels[i], adj = c(0, 0.5), 
                facing = "clockwise", niceFacing = TRUE,
                col = ct[labels[i]], cex = 0.7)
        }
})

suppressPackageStartupMessages(require(dendextend))
dend = color_branches(dend, k = 6, col = 1:6)

circos.trackPlotRegion(ylim = c(0, max_height), bg.border = NA, 
    track.height = 0.4, panel.fun = function(x, y) {
        circos.dendrogram(dend, max_height = max_height)
})
circos.clear()

eilslabs/circlize documentation built on May 16, 2019, 1:23 a.m.