Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.
Visualising phylogenies
(a personal view)
@rdmpage
http://iphylo.blogspot.com
Trees suck…
http://vimeo.com/26210611
…in ways that maps don’t
Maps are predictable
Navigation is predictable
Every pixel counts
Ground truth
Relative and absolute navigation
Latitude 42.363921
Longitude -71.087763
Phylogeny has none of this
There are few constraints on how
we can draw trees
X
A
B
C
D
Y
X
B
A
D
C
Y
We can reorder Y
@broadinstitute
X
B
A
D
C
Y
X is a partial order
X
B
A
D
C
Y
X is a partial order
X: evolutionary distance
B
A
D
C
Y
X: time
B
A
D
C
Y
Y
X
Z?
What would third dimension represent?
@wellcometrust
Pretty, but…
Is 3D useful?
@systbiol
Y:latitude
X:longitude
Z: evolutionary distance
@DavKidd @andrewxhill
@rdmpage
GenGIS
2D geographically
ordered tree
@rob_beiko
GenGIS-style trees on
Google Maps
@rdmpage
Challenges
• Does 3D have a role beyond being a gimmick?
• Geospatial phylogenies
Big trees
11 June 2003
“best viewed when enlarged to a 1.5-meter diameter”
add
@rdmpage
@rdmpage
OneZoom
http://tree.opentree.org
Challenges
• A visualisation of large trees that is as intuitive
and as useful as Google Maps
• A platform, not a picture
Touching the tree
@dr_pi
@kzelnio Think how great of a tool that could be at museums
on a large flat screen at 4 year old height.
Dendroscope
Build-a-Tree
https://lifeonearth.seas.harvard.edu/learning-activities/bat/
Challenges
• Intuitive, easy to use touchable trees
• Teaching and research
• Gamefication
Where are the trees?
http://www.treebase.org/
58
0
1000
2000
3000
4000
5000
6000
7000
1975 1980 1985 1990 1995 2000 2005
Year
Cumulativenumber
Rate of growth of phyloge...
Why aren’t we archiving these trees?
http://dx.doi.org/10.1371/journal.pbio.1001636 (2013)
Challenges
• Interactive trees for publications and
databases (eventually database = publication)
• Software to create pre...
Tree challenges
Big trees Touch Accessibility
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Visualing phylogenies: a personal view
Upcoming SlideShare
Loading in …5
×

Visualing phylogenies: a personal view

1,215 views

Published on

Talk given at Bivi2014

Published in: Science
  • Be the first to comment

Visualing phylogenies: a personal view

  1. 1. Visualising phylogenies (a personal view) @rdmpage http://iphylo.blogspot.com
  2. 2. Trees suck… http://vimeo.com/26210611
  3. 3. …in ways that maps don’t
  4. 4. Maps are predictable
  5. 5. Navigation is predictable
  6. 6. Every pixel counts
  7. 7. Ground truth
  8. 8. Relative and absolute navigation
  9. 9. Latitude 42.363921 Longitude -71.087763
  10. 10. Phylogeny has none of this
  11. 11. There are few constraints on how we can draw trees
  12. 12. X A B C D Y
  13. 13. X B A D C Y We can reorder Y
  14. 14. @broadinstitute
  15. 15. X B A D C Y X is a partial order
  16. 16. X B A D C Y X is a partial order
  17. 17. X: evolutionary distance B A D C Y
  18. 18. X: time B A D C Y
  19. 19. Y X Z? What would third dimension represent?
  20. 20. @wellcometrust
  21. 21. Pretty, but…
  22. 22. Is 3D useful?
  23. 23. @systbiol
  24. 24. Y:latitude X:longitude Z: evolutionary distance @DavKidd @andrewxhill
  25. 25. @rdmpage
  26. 26. GenGIS 2D geographically ordered tree @rob_beiko
  27. 27. GenGIS-style trees on Google Maps @rdmpage
  28. 28. Challenges • Does 3D have a role beyond being a gimmick? • Geospatial phylogenies
  29. 29. Big trees
  30. 30. 11 June 2003
  31. 31. “best viewed when enlarged to a 1.5-meter diameter”
  32. 32. add
  33. 33. @rdmpage
  34. 34. @rdmpage
  35. 35. OneZoom
  36. 36. http://tree.opentree.org
  37. 37. Challenges • A visualisation of large trees that is as intuitive and as useful as Google Maps • A platform, not a picture
  38. 38. Touching the tree
  39. 39. @dr_pi
  40. 40. @kzelnio Think how great of a tool that could be at museums on a large flat screen at 4 year old height.
  41. 41. Dendroscope
  42. 42. Build-a-Tree https://lifeonearth.seas.harvard.edu/learning-activities/bat/
  43. 43. Challenges • Intuitive, easy to use touchable trees • Teaching and research • Gamefication
  44. 44. Where are the trees?
  45. 45. http://www.treebase.org/
  46. 46. 58 0 1000 2000 3000 4000 5000 6000 7000 1975 1980 1985 1990 1995 2000 2005 Year Cumulativenumber Rate of growth of phylogenetic knowledge Number of papers with “molecular” and “phylogeny” in Web of Science Number of studies in TreeBASE
  47. 47. Why aren’t we archiving these trees? http://dx.doi.org/10.1371/journal.pbio.1001636 (2013)
  48. 48. Challenges • Interactive trees for publications and databases (eventually database = publication) • Software to create pretty, machine readable visualisations
  49. 49. Tree challenges Big trees Touch Accessibility

×