Design notes

We want an illustration tool that supports these goals:

• dynamic, data-driven illustration
• print-ready output (SVG => PDF, and possibly interactive versions)
• repeatable process (e.g., re-render after changes to data)
• shared expertise and "house styles" for journals or institutions
• rich possibilities for annotation and ornaments
• zero install, easy to get started

Our starting point is to think in terms of a decision cascade and rendering pipeline, as illustrated below (the editable doc is available on Google Drive):

This design separates decisions made at different times, by different users, and supports sharing and re-use. It sidesteps many important choices about data storage, social/sharing features, ownership and permissions. Our initial proof-of-concept tests will focus on the usability and output of this model with mocked data sources as input.

Initial notes gathered from stakeholders

web-based -- runs in modern browsers (based on support for d3/svg)

separation of “content” (the tree as a data structure and its associated information) and “layout/style” -- how the information should be rendered. E.g.

• rectangular vs circular layout of nodes/branches
• show branch support as numbers at nodes vs thickened branches over threshold
• render tip labels as taxon names (given mapping)
• more general mapping of selected data/attributes to styles?
  • to support, eg, rich edges (coded by color, thickness, linestyle)

figures can be saved as vector graphics (SVG)

• can the phylogenetic info be embedded in (saved with) the SVG, so that it could be round-tripped?
• or should SVG be treated as ephemeral, with separated tree data + style?
  • supports full round-tripping with updated external tree (as Newick, NeXML, …)

options for interactivity:

• zooming, panning
• “collapsible” clades
• “replay” (step through a series of zooms, pans, expanding/collapsing, …)

sharing styles

• browsable gallery of shared+named style settings
  • show each applied to a “generic” example tree
  • quickly choose and apply chosen style to your tree
• known-good styles, eg, “Radial layout with expressive links”
• “house styles” tailored for particular journals/venues
  • preferred typefaces
  • minimal line-weight at final printed size
  • eg, “Systematic Biology (print, b/w line art)”
  • eg, “FigShare slideshow w/ captions”

the BIG TREE problem and the need for a client-server API

• partial/selective rendering needed for big trees
• cannot rely on whole tree to fit into client’s memory
• need protocol for client to:
  • ask a server about resources (trees)
  • make (stateful?) requests to the server

integrate this into the Open Tree curation app, in Tools tab?

• easy selection of any tree in the current study
• choose and apply settings from Shared Styles
• link to full tree illustrator in a separate window?
• what is the result? maybe just facilitates opening this study’s tree(s) in the illustrator app?

usable from scripting languages = important [imho - RR]

some notes from the F2F meeting of larger Open Tree team [jimA]

• feature wish list
  • collapsing clades
  • highlighting clades
  • coloring clades
  • adding images
• COMPLETE SOLUTION w/o needing other graphics tools (survey question: "What do you use Illustrator for?")
• We absolutely need to interview a set of experts, ie, people who make nice tree figures “the hard way” through a more difficult workflow
• look for common feature set among the (many) existing tree-illustration tools
• focus on OCCASIONAL users, who need an easy-to-use tool
• look at possible interop INSTEAD of a major new tool?
  • use one or more of the (many) existing tree-graphic tools
  • help to modify/style output from these?
• offer option to label tree with original OR mapped taxon names?
• SPIRITED DISCUSSION! about whether journals have tricky formatting requirements for tree illustrations. What's the real deal?
• To elicit contributions, our value proposition is probably not The Ultimate Drawing Tool, more like the Path of Least Resistance:
  • dynamic (data-driven)
  • capture styles and illustration-specific decisions
  • really easy to use
  • good enough for publication