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Uploaded byTal Galili
2015 06-27 use-r2015_dendextend_tal_galili_01
This document appears to be a slide presentation about the dendextend R package. It begins with an outline of the talk including an example using the Iris dataset and overview of useful functions in the package. It then goes through various functions in more detail like labels, cutree, set and sending dendrograms to other packages. It emphasizes exploring and modifying dendrograms using dendextend and comparing dendrograms visually.
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2015 06-27 use-r2015_dendextend_tal_galili_01
- 1. Tal.Galili@gmail.com user!2015 - Thedendextend package
- 2. Tal.Galili@gmail.com Talk outline • Linkto this presentation + dendextend • 1 example • The most useful functions • Thanks!
- 3. Tal.Galili@gmail.com Getting this presentation Go to:www.R-statistics.com Or: just e-mail me:
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- 10. Tal.Galili@gmail.com The Iris dataset Usingheatmap.2 from gplots
- 11. Tal.Galili@gmail.com Why is “complete”different? Comparing 8 Clustering algorithms on The Iris dataset Using dendlist, cor.dendlist + The corrplot package
- 12. Tal.Galili@gmail.com Why is “complete”different?
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- 17. Tal.Galili@gmail.com Useful functions • labels •labels_colors • cutree • color_branches • sort • tanglegram • set (!)
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- 30. Tal.Galili@gmail.com https://plot.ly/~talgalili/ 6y/-sv-x/ Send adendrogram to plot.ly
- 31. Tal.Galili@gmail.com Send a dendrogramto d3heatmap Joint work with Joe Cheng
- 32. Tal.Galili@gmail.com Send a dendrogramto d3heatmap http://asbcllc.com/blog/ 2015_abn/enuj/14_15_pot_50lmth.xedni/pamtaeh_
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- 36. Tal.Galili@gmail.com hclust + pipes(via magrittr)
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- 38. Tal.Galili@gmail.com The set function set(dend,what, value) One function to rule them all!
- 39. 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
- 40. 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
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- 64. Tal.Galili@gmail.com Take-home messages: • hclust– is good for creating hierarchical clustering, but limited for plotting • dendrogram object • a nested list of lists • with attributes! • should be modified step by step before plotting • Dendrograms can be compared • Use dendextendRcpp for (“free”) speed
- 65. Tal.Galili@gmail.com Credits! dendextend This work wassupported 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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- 67. Tal.Galili@gmail.com The dendextend package Thankyou! for the slides: R-statistics.com
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- 70. Tal.Galili@gmail.com A dendrogram isa nested list of lists
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- 81. Tal.Galili@gmail.com Visually comparing twoclustering methods
- 82. Tal.Galili@gmail.com A plot froma recent HBP meeting in Lausanne Dendrogram Using 2 variables Dendrogram Using all variables
- 83. Tal.Galili@gmail.com Visually comparing twophylogenic trees
- 84. Tal.Galili@gmail.com Send a dendrogramto d3heatmap http://asbcllc.com/blog/ 2015_abn/enuj/14_15_pot_50lmth.xedni/pamtaeh_
- 85. Tal.Galili@gmail.com The dendextend package Thankyou! for the slides: R-statistics.com