Metadata elements
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? |
|
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
|
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
|
|
|
