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How to reorder dendrogram (R)?
2
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20 months ago
khaeuk • 70

Hello everyone! As my title says, I am having difficulty reordering my dendrogram. What I would like to do with my dendrogram is to flip two nodes along the y axis. For example,

enter image description here

How would I do this? I looked at reorder.dendrogram. But I don't quite get what it means and how you're suppose to do it, for most sources basically say the same thing as the manual page without any other examples/explanation. I tried messing around with 'weights' for reorder, but it wouldn't change my dendrogram. I tried looking other pages like, https://www.mail-archive.com/r-help@r-project.org/msg195536.html.

This is an example on the man page.

set.seed(123)

x <- rnorm(10)

hc <- hclust(dist(x))

dd <- as.dendrogram(hc)

dd.reorder <- reorder(dd, 10:1)

plot(dd, main = "random dendrogram 'dd'")

>

op <- par(mfcol = 1:2)

plot(dd.reorder, main = "reorder(dd, 10:1)")

plot(reorder(dd, 10:1, agglo.FUN = mean), main = "reorder(dd, 10:1, mean)")

par(op)

I don't know what that mfcol is but I tried changing the numbers, and it did swap some values, but I don't know how that works.

So next, I tried 'dendextend' package. I looked at the man page, seemed like there are some sort of ordering of the dendrogram, but more like ordering them in reverse or forward. So, my dendrogram would look like ...

enter image description here

Which is not what I'm looking for. Is there any other options? or is reorder.dendrogram is what i'm looking for, and i'm just not getting it? if so, can someone explain how it works?

Thank you!!

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1
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Hi,

have a look at my answer here:

heatmap.2 reorder branches

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17 months ago
Arnaud Ceol • 840
Milan, Italy

I've used a few time dendosort (https://f1000research.com/articles/3-177/v1 and https://cran.r-project.org/web/packages/dendsort/index.html), this is a nice library to sort your dendograms. You should have a look.

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2.3 years ago
Macherki M E • 120
Tunisia/ksour essef

I thinks that the dendrogram had the some order of user matrix input. In that way user will control the position of each vertice. If you wont separate a specific class statistically based on distance or graphically we have to reformulate data input.

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