how to draw circular dendrogram with distance information
1
1
Entering edit mode
3.5 years ago
agicict ▴ 160

I want draw circular dendrogram with R. I used dendextend package and followed example instructions.

However there is no description for annotatining height(distance) information. How to visualize height information?

Distance matrix

mat=matrix(abs(rnorm(100)),10,10);dimnames(mat)=list(letters[1:10],letters[1:10]) ma2=as.dist(mat)

dendrogram with distance info

hc=hclust(ma2)

dend=as.dendrogram(hc)

plot(dend)

Circular dendrogram without distance info (How to add height info for circular dendrogram?

library(dendextend)

circlize_dendrogram(dend = dend)

R • 2.6k views
ADD COMMENT
7
Entering edit mode
3.5 years ago

The function does not appear to draw the height axis for some reason. I have neither seen much examples of it online - all circular dendrograms appear to omit it. So, I embarked on a task to add it myself.

The following code appears to do it:

mat <- matrix(abs(rnorm(100)),10,10)
dimnames(mat) <- list(letters[1:10],letters[1:10])
ma2 <- as.dist(mat)
hc <- hclust(ma2)
dend <- as.dendrogram(hc)

par(mfrow=c(1,2))

plot(dend)

require(circlize)
require(dendextend)

#Get the heights for each branch
heights <- round(get_branches_heights(dend, sort=FALSE), 1)

#Get max height
maxHeight= max(heights)

#Set label and dendrogram height for circular dendrogram
labelHeight=0.1
dendHeight=0.8

#Draw the circular dendrogram
circlize_dendrogram(dend,
  facing = "outside",
  labels = TRUE,
  labels_track_height = labelHeight,
  dend_track_height = dendHeight)

# Create tick co-ordinates and values for the new axis
# We have to ensure that we don't overlap the label plot region
#   (height specified by labelHeight), nor the central region of the
#   plot (1-(dendHeight+labelHeight))
ticks <- seq(from = (1-(dendHeight+labelHeight)),
  to = (1-labelHeight), length.out=5)
values <- round(rev(seq(from=0, to=maxHeight, length.out=5)), 1)

#Add the new axis
require(plotrix)
ablineclip(h=0, v=ticks, col="black",
  x1=1-(dendHeight+labelHeight),
  x2=1-labelHeight,
  y1=0,
  y2=0.04,
  lwd=1.5)
text(ticks, 0+0.08, values, cex=0.8)
text(
  (1-labelHeight)-(((1-labelHeight)-(1-(dendHeight+labelHeight)))/2),
  0+0.14,
  "Height", cex=0.8)

Circular_Dendrogram

ADD COMMENT
1
Entering edit mode

What a wonderful solution! Thank you very much!

ADD REPLY
0
Entering edit mode

You're welcome! - thanks.

ADD REPLY

Login before adding your answer.

Traffic: 1675 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6