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nextstrain / auspice

Web app for visualizing pathogen evolution
https://docs.nextstrain.org/projects/auspice/
GNU Affero General Public License v3.0
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[maybe] differentiate between nodes with uncertainty vs nodes missing from colour scale #1797

Open jameshadfield opened 3 months ago

jameshadfield commented 3 months ago

Background

Nodes (branches & tips) will appear grey-er / de-saturated depending on their associated confidence/entropy, if available. Nodes (branches & tips) will be assigned a shade of grey if they are a non-continuous coloring where a colour scale has been provided however the node's value is not in the colour scale. It's very hard to distinguish between the two.

First raised in https://github.com/nextstrain/auspice/pull/1796:

[Jover] How would one be able to differentiate the grey scale for uncertainty vs grey scale for unprovided colorings? For example, imagine if zika's region had uncertainty, it would be mixed in with the "Asia" grey colorings.

[Trevor] The issue is that currently we use gray to mean either:

  • Unknown or uncertain
  • Uninteresting

This uninteresting take can be seen here https://nextstrain.org/ncov/gisaid/north-america/6m@2020-05-01 for example. This felt semantically appropriate to distinguish focal samples from background samples. I think this is okay however... This example does DTA on samples with a focal vs contextual color ramp so that uncertain nodes and contextual nodes are both gray. This feels okay and appropriate (perhaps not ideal, but not broken). It highlights clades that are more certain to be in a focal region.

Description

We could pick a different fallback colour palette where a colour-scale is provided but certain values are missing (either unintentionally or intentionally)

joverlee521 commented 3 months ago

Doesn't exactly solve the issue, but I like the idea of Value-Suppressing Uncertainty Palettes