jsm2015: the dendextend R package

Slides from the JSM 2015 talk by Tal Galili

Data & Analytics

Tal.Galili@gmail.com
The dendextend R package - JSM 2015

Tal.Galili@gmail.com
Talk outline
• Motivating example (Iris)
• Getting dendextend
• Functions for extending dendrogram
• Connections to other packages

Tal.Galili@gmail.com
The Iris dataset
Using: gplots::heatmap.2

Tal.Galili@gmail.com
Is there a difference between
clustering algorithms?

Tal.Galili@gmail.com
Why is “complete” different?
Comparing 8
Clustering algorithms on
The Iris dataset
Using: dendlist,
cor.dendlist +
The corrplot package

Tal.Galili@gmail.com
Why is “complete” different?
Using: tanglegram

Tal.Galili@gmail.com
Further reading
(includes the example)

Tal.Galili@gmail.com
dendextend paper in the
bioinformatics journal

Tal.Galili@gmail.com
Getting
the paper/presentation
Go to: www.R-statistics.com
Or: just e-mail me:

Tal.Galili@gmail.com
Some useful functions
for
extending dendrogram

Tal.Galili@gmail.com
Building a
dendrogram

Tal.Galili@gmail.com
Useful functions
• labels
• labels_colors
• cutree
• color_branches
• sort
• tanglegram
• set (!)

Tal.Galili@gmail.com
Using pipes
%>%
(but first…)

Tal.Galili@gmail.com
hclust + pipes (via magrittr)

Tal.Galili@gmail.com
Changing a
dendrogram

Tal.Galili@gmail.com
The set function
set(dend, what, value)
One function
to rule them all!

Tal.Galili@gmail.com
The set function
set(dend, what, value)
• dend a dendrogram
• what the property to update
• value new values to set in the tree

Tal.Galili@gmail.com
The set function
set(dend, what, value)
Type “what"
Labels labels, labels_to_character, labels_colors,
labels_cex, labels_to_character
Leaves leaves_pch, leaves_col, leaves_cex, hang_leaves
Nodes nodes_pch, nodes_col, nodes_cex
Branches branches_lty, branches_col, branches_lwd,
branches_k_color, by_labels_branches_lty,
by_labels_branches_col, by_labels_branches_lwd

Tal.Galili@gmail.com
useful
connections
to other
packages

Tal.Galili@gmail.com
https://plot.ly/~talgalili/ 6y/-sv-x/
ggplot2 + plot.ly

Tal.Galili@gmail.comJoint work with Joe Cheng
d3heatmap

Tal.Galili@gmail.com
http://asbcllc.com/blog/ 2015_abn/enuj/14_15_pot_50lmth.xedni/pamtaeh_
D3heatmap (zoomed)

Tal.Galili@gmail.com
Credits!
dendextend
This work was supported in part by the European Research Council under EC–EP7
European Research Council grant PSARPS-297519, and also by the HBP project.

Tal.Galili@gmail.com
Thank you!
for the slides:
R-statistics.com
The dendextend R package

Tal.Galili@gmail.com
Exploring a
dendrogram

Tal.Galili@gmail.com
A dendrogram is a nested list of lists

Tal.Galili@gmail.com
Depth-
First
Search

Tal.Galili@gmail.com
Comparing
dendrograms

Tal.Galili@gmail.com
tanglegram + untangle

Tal.Galili@gmail.com
“Correlation” measures

Tal.Galili@gmail.com
Modify nodes (no code)

Tal.Galili@gmail.com
dendextend
in the wild

Tal.Galili@gmail.com
Visually comparing two clustering methods

Tal.Galili@gmail.com
A plot from a recent HBP meeting in Lausanne
Dendrogram
Using 2
variables
Dendrogram
Using all
variables

Tal.Galili@gmail.com
Visually comparing two phylogenic trees

Tal.Galili@gmail.com
The dendextend R package
Thank you!
for the slides:
R-statistics.com

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