Visualization Needs

Owned by Naim Matasci
Last updated: May 16, 2012 by soliverVersion comment

Note: This is an initial draft.

Essential short-term needs (to support applications being currently implemented).

  • Non interactive (besides navigation, collapsing of clades, branch length, [shape])
  • Single trait support (overlaying multiple traits would require interactivity)

Visualization Needs:

  • Nodes:
    • Size
    • Color
    • Shape
    • Text labels
    • Pie chart
  • Branches/Edges
    • Variable lengths
    • Thickness
    • Text lables
    • Color
      • Solid
      • Gradient
  • Collapsed Wedges
    • Color
    • Gradient
    • divide wedge into sub-triangles that each can have a separate color
    • NOTE: Gradient and divided wedge may need to be calculated by TV

      multiple colors for collapsed clades (triangles) including:
      color of the triangle as function of the state of the tips: for continuous values a gradient from average at the tips to the value at the node
      [Suggestion: rank the n terminal taxa according to state value, splice triangle into n sections, color each section with gradient from tip to internal node.]
      subdivide the triangle in wedges matching the collapsed tips in color and proportion (e.g. if a collapsed clade contains 100 taxa, 40 of which have a status color-coded with red and 60 with yellow, the triangle should be colored so that 40% of the surface is red and the rest is yellow)

Export

  • SVG
  • PNG
  • JPG
  • Newick (data will be lost)
  • Newick Extended (data will probably be lost)
  • NexML
  • PhyloXML
  • Internal data models
    • for generating local copies of data and saving modified version of public data

Interactions

  • Context awareness: Clicking on item brings up contextual menu

    Contextual Menu: This is a definable menu based on metadata associated with tree. For example, clicking on an internal node brings up a menu with links that:

    • send all child-leaves to a program 'Sequence Extractor' to fetch the fasta sequences of the leaves
    • Regenerates a new tree of just that clade
    • Changes color of clade
    • Collapses clade into a wedge
    • Show/hide associated metadata (e.g. some trait)
  • Edges/Branches
  • Internal Nodes
    • Select all members in clade
    • Visualize just that clade
    • Leaves
  • Add information
    • Modify labels with new text
    • Add metadata
      • New traits
      • New annotations
      • New notes

Tree layout

  • Cladogram
    • Slanted
    • Rectangular
  • Phylogram
  • Re-root
  • Rootless
  • Ladderized
  • Replace underscores (_) in taxa names with whitespaces [search should proably support both]

Searching

  • Labels
    • node label
    • edge label
    • leaf label
  • Associated metadata (that is not visualized)
    • Annotations (GO, descriptive, traits)

Future needs

  • interactivity
    • interaction with objects to retrieve properties
  • support for multiple traits
  • images at nodes
  • basic tree interactions (through menu/toolbox)
    • selecting
    • pruning
    • subsetting
    • exporting
    • change visual properties
    • launch analyses
    • export
    • ...
  • flexible contextual menus at nodes, edges and selected subtrees to perform tree interactions
  • advanced tree manipulations
    • … TBD

To be discussed

  • Origin of the visual representation elements: in TE or in TV?
    • e.g. Pie charts for discrete traits
    1. Specify that information has to be represented as “pie chart” [thin lines for edges, no nodes, pie charts, legend]
    2. Define colors of sections
    3. Draw pie charts