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jsm2015: the dendextend R package
1.
Tal.Galili@gmail.com The dendextend R
package - JSM 2015
2.
Tal.Galili@gmail.com Talk outline • Motivating
example (Iris) • Getting dendextend • Functions for extending dendrogram • Connections to other packages
3.
Tal.Galili@gmail.com Motivating example
4.
Tal.Galili@gmail.com The Iris dataset
5.
Tal.Galili@gmail.com The Iris dataset
6.
Tal.Galili@gmail.com The Iris dataset
7.
Tal.Galili@gmail.com The Iris dataset Using:
gplots::heatmap.2
8.
Tal.Galili@gmail.com Is there a
difference between clustering algorithms?
9.
Tal.Galili@gmail.com Why is “complete”
different? Comparing 8 Clustering algorithms on The Iris dataset Using: dendlist, cor.dendlist + The corrplot package
10.
Tal.Galili@gmail.com Why is “complete”
different? Using: tanglegram
11.
Tal.Galili@gmail.com Getting dendextend
12.
Tal.Galili@gmail.com
13.
Tal.Galili@gmail.com Further reading (includes the
example)
14.
Tal.Galili@gmail.com dendextend paper in
the bioinformatics journal
15.
Tal.Galili@gmail.com Getting the paper/presentation Go to:
www.R-statistics.com Or: just e-mail me:
16.
Tal.Galili@gmail.com Some useful functions for extending
dendrogram
17.
Tal.Galili@gmail.com Building a dendrogram
18.
Tal.Galili@gmail.com hclust -> dend
19.
Tal.Galili@gmail.com hclust -> dend
20.
Tal.Galili@gmail.com Useful functions • labels •
labels_colors • cutree • color_branches • sort • tanglegram • set (!)
21.
Tal.Galili@gmail.com
22.
Tal.Galili@gmail.com
23.
Tal.Galili@gmail.com
24.
Tal.Galili@gmail.com
25.
Tal.Galili@gmail.com
26.
Tal.Galili@gmail.com
27.
Tal.Galili@gmail.com
28.
Tal.Galili@gmail.com
29.
Tal.Galili@gmail.com
30.
Tal.Galili@gmail.com
31.
Tal.Galili@gmail.com ONE more function
32.
Tal.Galili@gmail.com Using pipes %>% (but first…)
33.
Tal.Galili@gmail.com hclust -> dend
34.
Tal.Galili@gmail.com hclust + pipes
(via magrittr)
35.
Tal.Galili@gmail.com Changing a dendrogram
36.
Tal.Galili@gmail.com The set function set(dend,
what, value) One function to rule them all!
37.
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
38.
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
39.
Tal.Galili@gmail.com A dend exmaple
40.
Tal.Galili@gmail.com Modify labels
41.
Tal.Galili@gmail.com
42.
Tal.Galili@gmail.com
43.
Tal.Galili@gmail.com Modify branches
44.
Tal.Galili@gmail.com Modify branches
45.
Tal.Galili@gmail.com Modify nodes
46.
Tal.Galili@gmail.com useful connections to other packages
47.
Tal.Galili@gmail.com circlize
48.
Tal.Galili@gmail.com ggplot2
49.
Tal.Galili@gmail.com ggplot2
50.
Tal.Galili@gmail.com https://plot.ly/~talgalili/ 6y/-sv-x/ ggplot2 +
plot.ly
51.
Tal.Galili@gmail.com gplots::heatmap.2
52.
Tal.Galili@gmail.comJoint work with
Joe Cheng d3heatmap
53.
Tal.Galili@gmail.com http://asbcllc.com/blog/ 2015_abn/enuj/14_15_pot_50lmth.xedni/pamtaeh_ D3heatmap (zoomed)
54.
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.
55.
Tal.Galili@gmail.com Thank you! for the
slides: R-statistics.com The dendextend R package
56.
Tal.Galili@gmail.com Exploring a dendrogram
57.
Tal.Galili@gmail.com
58.
Tal.Galili@gmail.com A dendrogram is
a nested list of lists
59.
Tal.Galili@gmail.com
60.
Tal.Galili@gmail.com
61.
Tal.Galili@gmail.com Depth- First Search
62.
Tal.Galili@gmail.com Depth- First Search
63.
Tal.Galili@gmail.com Comparing dendrograms
64.
Tal.Galili@gmail.com tanglegram + untangle
65.
Tal.Galili@gmail.com tanglegram + untangle
66.
Tal.Galili@gmail.com “Correlation” measures
67.
Tal.Galili@gmail.com “Correlation” measures
68.
Tal.Galili@gmail.com Rotate branches
69.
Tal.Galili@gmail.com
70.
Tal.Galili@gmail.com Modify nodes (no
code)
71.
Tal.Galili@gmail.com
72.
Tal.Galili@gmail.com
73.
Tal.Galili@gmail.com
74.
Tal.Galili@gmail.com Rotate branches
75.
Tal.Galili@gmail.com Prune branches
76.
Tal.Galili@gmail.com Prune branches
77.
Tal.Galili@gmail.com Add rectangles
78.
Tal.Galili@gmail.com Add rectangles
79.
Tal.Galili@gmail.com
80.
Tal.Galili@gmail.com dendextend in the wild
81.
Tal.Galili@gmail.com Visually comparing two
clustering methods
82.
Tal.Galili@gmail.com A plot from
a recent HBP meeting in Lausanne Dendrogram Using 2 variables Dendrogram Using all variables
83.
Tal.Galili@gmail.com Visually comparing two
phylogenic trees
84.
Tal.Galili@gmail.com The dendextend R
package Thank you! for the slides: R-statistics.com
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