Slides from the JSM 2015 talk by Tal Galili

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The dendextend R package - JSM 2015

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Talk outline
• Motivating example (Iris)
• Getting dendextend
• Functions for extending dendrogram
• Connections to other packages

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Motivating
example

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The Iris dataset

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The Iris dataset

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The Iris dataset

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The Iris dataset
Using: gplots::heatmap.2

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Is there a difference between
clustering algorithms?

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

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Why is “complete” different?
Using: tanglegram

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Getting
dendextend

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Further reading
(includes the example)

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dendextend paper in the
bioinformatics journal

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

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Some useful functions
for
extending dendrogram

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Building a
dendrogram

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hclust -> dend

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hclust -> dend

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Useful functions
• labels
• labels_colors
• cutree
• color_branches
• sort
• tanglegram
• set (!)

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ONE more
function

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Using pipes
%>%
(but first…)

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hclust -> dend

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hclust + pipes (via magrittr)

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Changing a
dendrogram

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The set function
set(dend, what, value)
One function
to rule them all!

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The set function
set(dend, what, value)
• dend a dendrogram
• what the property to update
• value new values to set in the tree

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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

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A dend exmaple

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Modify labels

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Modify branches

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Modify branches

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Modify nodes

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useful
connections
to other
packages

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circlize

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ggplot2

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ggplot2

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https://plot.ly/~talgalili/ 6y/-sv-x/
ggplot2 + plot.ly

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gplots::heatmap.2

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d3heatmap

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

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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.

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Thank you!
for the slides:
R-statistics.com
The dendextend R package

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Exploring a
dendrogram

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A dendrogram is a nested list of lists

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Depth-
First
Search

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Depth-
First
Search

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Comparing
dendrograms

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tanglegram + untangle

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tanglegram + untangle

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“Correlation” measures

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“Correlation” measures

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Rotate branches

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Modify nodes (no code)

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Rotate branches

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Prune branches

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Prune branches

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Add rectangles

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Add rectangles

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dendextend
in the wild

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Visually comparing two clustering methods

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A plot from a recent HBP meeting in Lausanne
Dendrogram
Using 2
variables
Dendrogram
Using all
variables

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Visually comparing two phylogenic trees

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The dendextend R package
Thank you!
for the slides:
R-statistics.com