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Web: Grey scale coloring for region/country/divison if scale not predefined in reference tree #1265
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I was wondering why the "Unknown" value wasn't automatically ignored by Auspice and found this was done on purpose! nextclade/packages_rs/nextclade/src/tree/tree.rs Lines 21 to 23 in ca54ba3
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Thanks Jover! Since the beginning, we've been trying to carefully ignore the country and other values, because Nextclade inputs and, therefore, newly attached tree nodes simply don't have this information. My understanding is that in our own datasets we don't have these fields, and so these colorings do not even appear in the dropdown. I had to add the handling of unknown values long time ago for the reasons I don't remember clearly, but I found this Slack thread: But maybe it needs to be revisited. You know more about this things. What can you recommend? |
Ah, the grey scale is the intended behavior in Auspice for values that are not defined in the color scale. Maybe the easiest thing to do here would be for Nextclade to use |
We have never been very careful about metadata other than clades on these trees. But many datasets 'inherit' these metadata attributes from the workflows they are based on. I don't think I fully understand the problem yet though. If I look at these trees in auspice (outside of nextclade) they get assigned the default rainbow colors. Is it that only after adding the fake I don't remember all the reasons why we wanted to avoid auspice interpreting this as |
Yes, Nextclade injects a single color scale for the added Using the Influenza H1N1pdm HA dataset as an example, the "Region" color-by looks fine because tree.json includes a scale for region. However, the "Country" color-by is grey scale because the tree.json does not define a scale for country. |
It's not clear to me if this should be considered a bug or user-error but at least wanted to document the behavior here.
If the reference tree for a Nextclade dataset does not pre-define the color scale for region, country, or division fields, then coloring becomes grey scale due to the injection of the "Unknown" value scale
nextclade/packages_rs/nextclade/src/tree/tree_preprocess.rs
Lines 282 to 283 in aaac7ce
This was first reported in Nextstrain office hours on 2023-09-21 by an external user who built their own Nextclade datasets, but can be observed in the "official" Influenza A H1N1pdm HA dataset which does not define the color scale for "country":
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