[email protected] user!2015 - the dendextend package
TRANSCRIPT
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Talk outline• Link to this presentation + dendextend
• 1 example
• The most useful functions
• Thanks!
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Getting this presentation
Go to: www.R-statistics.comOr: just e-mail me:
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Why is “complete” different?
Comparing 8 Clustering algorithms onThe Iris dataset
Using dendlist,cor.dendlist + The corrplot package
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Useful functions• labels• labels_colors• cutree• color_branches• sort• tanglegram• set (!)
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https://plot.ly/~talgalili/6/y-vs-x/
Send a dendrogram to plot.ly
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Send a dendrogram to d3heatmap
http://asbcllc.com/blog/2015/june/nba_14_15_top_50_heatmap/index.html
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The set functionset(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 functionset(dend, what, value)
Type “what"Labels labels, labels_to_character, labels_colors,
labels_cex, labels_to_characterLeaves leaves_pch, leaves_col, leaves_cex, hang_leavesNodes 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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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
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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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A plot from a recent HBP meeting in Lausanne
DendrogramUsing 2 variables
DendrogramUsing all variables
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Send a dendrogram to d3heatmap
http://asbcllc.com/blog/2015/june/nba_14_15_top_50_heatmap/index.html