circlize_dendrogram: Plot a circlized dendrograms

In dendextend: Extending 'dendrogram' Functionality in R

Plot a circlized dendrograms

Description

Plot a circlized dendrograms using the circlize package (must be installed for the function to work).

This type of plot is also sometimes called fan tree plot (although the name fan-plot is also used for a different plot in time series analysis), radial tree plot, polar tree plot, circular tree plot, and probably other names as well.

An advantage for using the circlize package directly is for plotting a circular dendrogram so that you can add more graphics for the elements in the tree just by adding more tracks using circos.track.

Usage

circlize_dendrogram(
  dend,
  facing = c("outside", "inside"),
  labels = TRUE,
  labels_track_height = 0.1,
  dend_track_height = 0.5,
  ...
)

Arguments

dend	a dendrogram object
facing	Is the dendromgrams facing inside to the circle or outside.
labels	logical (TRUE) - should the labels be plotted as well.
labels_track_height	a value for adjusting the room for the labels. It is 0.2 by default, but if NULL or NA, it will adjust automatically based on the max width of the labels. However, if this is too long, the plot will give an error: Error in check.track.position(track.index, track.start, track.height) : not enough space for cells at track index '2'.
dend_track_height	a value for adjusting the room for the dendrogram.
...	Ignored.

Value

The dend that was used for plotting.

Author(s)

Zuguang Gu, Tal Galili

Source

This code is based on the work of Zuguang Gu. If you use the function, please cite both dendextend (see: citation("dendextend")), as well as the circlize package (see: citation("circlize")).

See Also

circos.dendrogram

Examples

## Not run: 

dend <- iris[1:40, -5] %>%
  dist() %>%
  hclust() %>%
  as.dendrogram() %>%
  set("branches_k_color", k = 3) %>%
  set("branches_lwd", c(5, 2, 1.5)) %>%
  set("branches_lty", c(1, 1, 3, 1, 1, 2)) %>%
  set("labels_colors") %>%
  set("labels_cex", c(.9, 1.2)) %>%
  set("nodes_pch", 19) %>%
  set("nodes_col", c("orange", "black", "plum", NA))

circlize_dendrogram(dend)
circlize_dendrogram(dend, labels = FALSE)
circlize_dendrogram(dend, facing = "inside", labels = FALSE)


# In the following we get the dendrogram but can also get extra information on top of it
circos.initialize("foo", xlim = c(0, 40))
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
  circos.rect(1:40 - 0.8, rep(0, 40), 1:40 - 0.2, runif(40), col = rand_color(40), border = NA)
}, bg.border = NA)
circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
  circos.text(1:40 - 0.5, rep(0, 40), labels(dend),
    col = labels_colors(dend),
    facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5)
  )
}, bg.border = NA, track.height = 0.1)
max_height <- attr(dend, "height")
circos.track(ylim = c(0, max_height), panel.fun = function(x, y) {
  circos.dendrogram(dend, max_height = max_height)
}, track.height = 0.5, bg.border = NA)
circos.clear()

## End(Not run)

dendextend documentation built on Oct. 13, 2024, 1:06 a.m.