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.  

   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