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For the purpose of visualization, we need a true presentation syntax separate from what the colours, branch widths, etc. mean biologically. At the core we're talking about a simple controlled vocabulary elements such as branch colours, node icons, etc. This would allow us to attach metadata to nodes, branches, trees, etc in NeXML. We just need to find agreement on the namespace that we want to put these terms in, and their value space (pixels? points? how are colours encoded?).

Visual elements we want to include can be divided two ways - into the location (i.e. on nodes, on branches, on tips) and the element type (colours, shapes, sizes, text, URLs). Not all attributes may be logical in all locations.

  • branches
    • colour (1-2 per branch, allow for gradient)
    • width
    • style (dotted, dashed, etc.)
    • text label
  • nodes
    • icon (size, shape)
    • colour
    • images
    • pie diagrams (probably not imported as an image)
  • clades (all descendants of a node)
    • colour (of all branches)
    • highlighting (colour block)
    • proportional coloring to represent diversity in colors of underlying taxa
  • text offset/font/text-decoration (italic, bold, underlined)
  • collapsed clades
  • clickable URLs

Metadata feature

Data type

Representation options

Issues

Category (e.g., a trait category)

Categorical data (discrete values)

Discrete colors

- How many different categories required? 
- Small number of unique colors reliably distinguishable

Category (e.g., a trait category)

Categorical data (discrete values )

Glyphs, applied to:

Need to ensure that glyphs are distinguishable

Continuous magnitude or value, positive values (e.g., degree to which a clade contains species with a particular trait)

Continuous data

Color map applied to

  • edge
  • node
  • clade
  • text
  • text background
  • heat map cell
    Width applied to:
  • branch

Luminance (or, to a much lesser degree, saturation) component required to represent magnitude information.  E.g., Heated body color map.

Continuous magnitude or value, positive values (e.g., degree to which a clade contains species with a particular trait)

Continuous data, segmented into discrete ranges

Segmented color map applied to

  • edge
  • node
  • clade
  • text
  • text background
  • heat map cell


 

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1 Comment

  1. Looks good. I wouldn't limit colors to branch to <=2, though -- think of doing stochastic character mapping -- things could change multiple times on Amborella branch. Or, if color is used to show time intervals (Eocene, Oligocene, etc.) one branch might be in more than two intervals.

    Also, might you want to put images on branches as well as nodes? Simple example is a hash mark for a character change, but maybe other things, too (image of a fossil used to date stem group placed at its appropriate time, for example).

    For branch width, would you want ability to vary width along the branch? For instance, gene tree-species tree, where you could have a model with pop size slowly increasing along a branch (allowed in star-BEAST). Could help the tree reconciliation group.