tal.galili@gmail.com user!2015 - the dendextend package
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Tal.Galili@gmail.com
user!2015 - The dendextend package
Tal.Galili@gmail.com
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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Getting dendextend
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Further reading
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Further reading
(1 example - no code)
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The Iris dataset
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The Iris dataset
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The Iris dataset
Using heatmap.2 from gplots
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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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Why is “complete” different?
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Back tobasics
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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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2 useful connections
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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
Joint work with Joe Cheng
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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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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 functionset(dend, what, value)
One function to rule them all!
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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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A dend exmaple
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Modify labels
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Modify nodes (no code)
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Modify nodes (no code)
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Modify branches
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Modify branches
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Rotate branches
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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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dendextendand other packages
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Gplots: heatmap.2
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dynamicTreeCut
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pvclust
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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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Credits!
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The dendextend package
Thank you!for the slides:
R-statistics.com
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Exploring a dendrogram
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A dendrogram is a nested list of lists
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Depth- FirstSearch
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Depth- FirstSearch
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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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dendextendin the wild
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Visually comparing two clustering methods
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A plot from a recent HBP meeting in Lausanne
DendrogramUsing 2 variables
DendrogramUsing all variables
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Visually comparing two phylogenic trees
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Send a dendrogram to d3heatmap
http://asbcllc.com/blog/2015/june/nba_14_15_top_50_heatmap/index.html
Tal.Galili@gmail.com
The dendextend package
Thank you!for the slides:
R-statistics.com
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