2015 06-27 use-r2015_dendextend_tal_galili_01
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A useR!2015 presentation about dendextend
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2015 06-27 use-r2015_dendextend_tal_galili_01
- 1. Tal.Galili@gmail.com user!2015 - The dendextend package
- 2. Tal.Galili@gmail.com Talk outline • Link to 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:
- 7. Tal.Galili@gmail.com Further reading (1 example - no code)
- 10. Tal.Galili@gmail.com The Iris dataset Using heatmap.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?
- 17. Tal.Galili@gmail.com Useful functions • labels • labels_colors • cutree • color_branches • sort • tanglegram • set (!)
- 30. Tal.Galili@gmail.com https://plot.ly/~talgalili/ 6y/-sv-x/ Send a dendrogram to plot.ly
- 31. Tal.Galili@gmail.com Send a dendrogram to d3heatmap Joint work with Joe Cheng
- 32. Tal.Galili@gmail.com Send a dendrogram to d3heatmap http://asbcllc.com/blog/ 2015_abn/enuj/14_15_pot_50lmth.xedni/pamtaeh_
- 36. Tal.Galili@gmail.com hclust + pipes (via magrittr)
- 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
- 47. Tal.Galili@gmail.com Modify nodes (no code)
- 48. Tal.Galili@gmail.com Modify nodes (no code)
- 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 was supported in part by the European Research Council under EC–EP7 European Research Council grant PSARPS-297519, and also by the HBP project.
- 67. Tal.Galili@gmail.com The dendextend package Thank you! for the slides: R-statistics.com
- 70. Tal.Galili@gmail.com A dendrogram is a nested list of lists
- 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 Send a dendrogram to d3heatmap http://asbcllc.com/blog/ 2015_abn/enuj/14_15_pot_50lmth.xedni/pamtaeh_
- 85. Tal.Galili@gmail.com The dendextend package Thank you! for the slides: R-statistics.com