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Tal.Galili@gmail.com
The dendextend R package - JSM 2015
Tal.Galili@gmail.com
Talk outline
• Motivating example (Iris)
• Getting dendextend
• Functions for extending dendrogram
• ...
Tal.Galili@gmail.com
Motivating
example
Tal.Galili@gmail.com
The Iris dataset
Tal.Galili@gmail.com
The Iris dataset
Tal.Galili@gmail.com
The Iris dataset
Tal.Galili@gmail.com
The Iris dataset
Using: gplots::heatmap.2
Tal.Galili@gmail.com
Is there a difference between
clustering algorithms?
Tal.Galili@gmail.com
Why is “complete” different?
Comparing 8
Clustering algorithms on
The Iris dataset
Using: dendlist,
c...
Tal.Galili@gmail.com
Why is “complete” different?
Using: tanglegram
Tal.Galili@gmail.com
Getting
dendextend
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Further reading
(includes the example)
Tal.Galili@gmail.com
dendextend paper in the
bioinformatics journal
Tal.Galili@gmail.com
Getting
the paper/presentation
Go to: www.R-statistics.com
Or: just e-mail me:
Tal.Galili@gmail.com
Some useful functions
for
extending dendrogram
Tal.Galili@gmail.com
Building a
dendrogram
Tal.Galili@gmail.com
hclust -> dend
Tal.Galili@gmail.com
hclust -> dend
Tal.Galili@gmail.com
Useful functions
• labels
• labels_colors
• cutree
• color_branches
• sort
• tanglegram
• set (!)
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
ONE more
function
Tal.Galili@gmail.com
Using pipes
%>%
(but first…)
Tal.Galili@gmail.com
hclust -> dend
Tal.Galili@gmail.com
hclust + pipes (via magrittr)
Tal.Galili@gmail.com
Changing a
dendrogram
Tal.Galili@gmail.com
The set function
set(dend, what, value)
One function
to rule them all!
Tal.Galili@gmail.com
The set function
set(dend, what, value)
• dend a dendrogram
• what the property to update
• value new...
Tal.Galili@gmail.com
The set function
set(dend, what, value)
Type “what"
Labels labels, labels_to_character, labels_colors...
Tal.Galili@gmail.com
A dend exmaple
Tal.Galili@gmail.com
Modify labels
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Modify branches
Tal.Galili@gmail.com
Modify branches
Tal.Galili@gmail.com
Modify nodes
Tal.Galili@gmail.com
useful
connections
to other
packages
Tal.Galili@gmail.com
circlize
Tal.Galili@gmail.com
ggplot2
Tal.Galili@gmail.com
ggplot2
Tal.Galili@gmail.com
https://plot.ly/~talgalili/ 6y/-sv-x/
ggplot2 + plot.ly
Tal.Galili@gmail.com
gplots::heatmap.2
Tal.Galili@gmail.comJoint work with Joe Cheng
d3heatmap
Tal.Galili@gmail.com
http://asbcllc.com/blog/ 2015_abn/enuj/14_15_pot_50lmth.xedni/pamtaeh_
D3heatmap (zoomed)
Tal.Galili@gmail.com
Credits!
dendextend
This work was supported in part by the European Research Council under EC–EP7
Eur...
Tal.Galili@gmail.com
Thank you!
for the slides:
R-statistics.com
The dendextend R package
Tal.Galili@gmail.com
Exploring a
dendrogram
Tal.Galili@gmail.com
Tal.Galili@gmail.com
A dendrogram is a nested list of lists
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Depth-
First
Search
Tal.Galili@gmail.com
Depth-
First
Search
Tal.Galili@gmail.com
Comparing
dendrograms
Tal.Galili@gmail.com
tanglegram + untangle
Tal.Galili@gmail.com
tanglegram + untangle
Tal.Galili@gmail.com
“Correlation” measures
Tal.Galili@gmail.com
“Correlation” measures
Tal.Galili@gmail.com
Rotate branches
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Modify nodes (no code)
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Tal.Galili@gmail.com
Rotate branches
Tal.Galili@gmail.com
Prune branches
Tal.Galili@gmail.com
Prune branches
Tal.Galili@gmail.com
Add rectangles
Tal.Galili@gmail.com
Add rectangles
Tal.Galili@gmail.com
Tal.Galili@gmail.com
dendextend
in the wild
Tal.Galili@gmail.com
Visually comparing two clustering methods
Tal.Galili@gmail.com
A plot from a recent HBP meeting in Lausanne
Dendrogram
Using 2
variables
Dendrogram
Using all
variab...
Tal.Galili@gmail.com
Visually comparing two phylogenic trees
Tal.Galili@gmail.com
The dendextend R package
Thank you!
for the slides:
R-statistics.com
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jsm2015: the dendextend R package

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Slides from the JSM 2015 talk by Tal Galili

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jsm2015: the dendextend R package

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

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