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Reimplement clade graph rendering #13

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@ivan-aksamentov ivan-aksamentov commented Nov 2, 2022 •
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This aims to reimplement rendering logic of the schema without using D3.js, such that we have more control on the schema layout.

  • remove d3.js DOM functions, use React instead
  • convert clades.json to a new format that can support recombination
  • reimplement graph construction (calculate node and edge positions), without using d3.js hierarchy functions: in particular allowing multiple parents (to show recombination relationships), and perhaps arbitrary graphs in general
  • render various attributes of nodes and edges (to be discussed) - using text, tooltips, graphics, color, animation etc
  • size nodes according to some metric (e.g. total number of observed sequences)
  • render the graph into an SVG file, for static usage
  • package the interactive React components into an NPM package, to be used in React apps where we currently use the static SVG (Nextclade, CoVariants, perhaps on Nextstrain.org somewhere as well)
  • CI: automatically release SVGs to GitHub Releases
  • CI: automatically release NPM package

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@ivan-aksamentov ivan-aksamentov changed the title Reimplement rendering Reimplement clade graph rendering Nov 2, 2022
@ivan-aksamentov
feat: convert clades.json tree into a graph
fe91614 
Here I  add a script to "flatten" the object hierarchy in `clades.json` into 2 lists: `nodes` and `edges` that represent the same hierarchy in a different way.

Every node now has an `id` (an arbitrary string). Every edge is directional and refers to its `source` and `target` noes by the node `id`. This representation will allow us to build arbitrary directed graphs instead of just trees (in particular, to allow showing recombinant relationships between clades)

I also split the composite Nextstrain name strings into the clade, lineages, who variant and other components. This should allows a richer display.
@ivan-aksamentov ivan-aksamentov force-pushed the feat/rendering-reloaded branch from 5ec79d2 to fe91614 Compare November 2, 2022 20:57
@ivan-aksamentov ivan-aksamentov mentioned this pull request Nov 21, 2024
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