Jun 102015
 

Visualizing one or more trees/taxonomies with non-trivial number of characters and taxa is a challenge a number of projects is facing. The ETC project organized a workshop with information visualization experts, data providers (trees and characters), and end users to tackle the challenge together.
The meeting was organized by Hong Cui and hosted by Bertram Ludäscher in the National Center for Supercomputing Applications (NCSA), Urbana, IL, in May 11-13. Phenotype RCN participants Matt Yoder, Nico Franz and Martín Ramírez attended the meeting and posed vis challenges. Much of the workshop was devoted to brainstorm on the challenge of representing a large dataset together with some kind of mapping on a tree, and often on two trees simultaneously. This is a familiar challenge for anatomy ontologists, who are trying to represent the interaction of phylogenetic trees, matrices and ontologies:

Right, the level of anatomical data available for different parts of the fin and limb can be visualized for taxa along the fin to limb transition (figure from Dececchi et al. in press 2015, Systematic Biology, doi: 10.1093/sysbio/syv031). Left, a phylogeny of spiders colored according to anatomical complexity, derived from the ontology (figure from Ramírez & Michalik 2014, doi: 10.1111/cla.12075).

Right, the level of anatomical data available for different parts of the fin and limb can be visualized for taxa along the fin to limb transition (figure from Dececchi et al. in press 2015, Systematic Biology, doi: 10.1093/sysbio/syv031). Left, a phylogeny of spiders colored according to anatomical complexity, derived from the ontology (figure from Ramírez & Michalik 2014, doi: 10.1111/cla.12075).


The beautiful and clever examples presented by the vis experts were inspiring. How these gorgeous examples can help us represent or complex data in intuitive visualizations? Filters, sort controls, heat maps, zoom panes, collapsing, expanding, and more tools – all made in us two effects: Make some of our challenges look feasible, and refine our vague ideas into more precise challenges.
Hierarchical Circular Layouts, or HCL (Dang, Murray, and Forbes 2015), uses circular layouts on a hierarchical structure.

Hierarchical Circular Layouts, or HCL (Dang, Murray, and Forbes 2015), uses circular layouts on a hierarchical structure.


PathwayMatrix: Visualizing Binary Relationships between Proteins in Biological Pathways (Dang, Murray, and Forbes, 2015). PathwayMatrix can be used not only for biological pathway visualization, but also for character and taxon data.  See: http://biovis.net/year/2015/papers/pathwaymatrix-visualizing-binary-relationships-between-proteins-biological-pathways

PathwayMatrix: Visualizing Binary Relationships between Proteins in Biological Pathways (Dang, Murray, and Forbes, 2015). PathwayMatrix can be used not only for biological pathway visualization, but also for character and taxon data. See: http://biovis.net/year/2015/papers/pathwaymatrix-visualizing-binary-relationships-between-proteins-biological-pathways


The ETC project will implement a few promising techniques as part of ETC toolkit to invite comments and suggestions from broader communities. Stay tuned, and crunch your data into nice visualizations!
(post by Martin Ramírez)

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