Visualization Needs
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
-
- Specify that information has to be represented as “pie chart” [thin lines for edges, no nodes, pie charts, legend]
- Define colors of sections
- Draw pie charts