A useR!2015 presentation about dendextend

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:

4. Tal.Galili@gmail.com
Getting
dendextend

5. Tal.Galili@gmail.com

6. Tal.Galili@gmail.com
Further reading

7. Tal.Galili@gmail.com
Further reading
(1 example - no code)

8. Tal.Galili@gmail.com
The Iris dataset

9. Tal.Galili@gmail.com
The Iris dataset

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?

13. Tal.Galili@gmail.com
Back to
basics

14. Tal.Galili@gmail.com
Building a
dendrogram

15. Tal.Galili@gmail.com
hclust -> dend

16. Tal.Galili@gmail.com
hclust -> dend

17. Tal.Galili@gmail.com
Useful functions
• labels
• labels_colors
• cutree
• color_branches
• sort
• tanglegram
• set (!)

18. Tal.Galili@gmail.com

19. Tal.Galili@gmail.com

20. Tal.Galili@gmail.com

21. Tal.Galili@gmail.com

22. Tal.Galili@gmail.com

23. Tal.Galili@gmail.com

24. Tal.Galili@gmail.com

25. Tal.Galili@gmail.com

26. Tal.Galili@gmail.com

27. Tal.Galili@gmail.com
2 useful
connections

28. Tal.Galili@gmail.com

29. Tal.Galili@gmail.com

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_

33. Tal.Galili@gmail.com
ONE more
function

34. Tal.Galili@gmail.com
Using pipes
%>%
(but first…)

35. Tal.Galili@gmail.com
hclust -> dend

36. Tal.Galili@gmail.com
hclust + pipes (via magrittr)

37. Tal.Galili@gmail.com
Changing a
dendrogram

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

41. Tal.Galili@gmail.com
A dend exmaple

42. Tal.Galili@gmail.com
Modify labels

43. Tal.Galili@gmail.com

44. Tal.Galili@gmail.com

45. Tal.Galili@gmail.com

46. Tal.Galili@gmail.com

47. Tal.Galili@gmail.com
Modify nodes (no code)

48. Tal.Galili@gmail.com
Modify nodes (no code)

49. Tal.Galili@gmail.com
Modify branches

50. Tal.Galili@gmail.com
Modify branches

51. Tal.Galili@gmail.com

52. Tal.Galili@gmail.com

53. Tal.Galili@gmail.com

54. Tal.Galili@gmail.com
Rotate branches

55. Tal.Galili@gmail.com
Rotate branches

56. Tal.Galili@gmail.com
Prune branches

57. Tal.Galili@gmail.com
Prune branches

58. Tal.Galili@gmail.com
Add rectangles

59. Tal.Galili@gmail.com
Add rectangles

60. Tal.Galili@gmail.com
dendextend
and other packages

61. Tal.Galili@gmail.com
Gplots: heatmap.2

62. Tal.Galili@gmail.com
dynamicTreeCut

63. Tal.Galili@gmail.com
pvclust

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.

66. Tal.Galili@gmail.com
Credits!

67. Tal.Galili@gmail.com
The dendextend package
Thank you!
for the slides:
R-statistics.com

68. Tal.Galili@gmail.com
Exploring a
dendrogram

69. Tal.Galili@gmail.com

70. Tal.Galili@gmail.com
A dendrogram is a nested list of lists

71. Tal.Galili@gmail.com

72. Tal.Galili@gmail.com

73. Tal.Galili@gmail.com
Depth-
First
Search

74. Tal.Galili@gmail.com
Depth-
First
Search

75. Tal.Galili@gmail.com
Comparing
dendrograms

76. Tal.Galili@gmail.com
tanglegram + untangle

77. Tal.Galili@gmail.com
tanglegram + untangle

78. Tal.Galili@gmail.com
“Correlation” measures

79. Tal.Galili@gmail.com
“Correlation” measures

80. Tal.Galili@gmail.com
dendextend
in the wild

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