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Add segment-specific Auspice configs for 2y builds
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Adds segment-specific Auspice config JSONs for 2y builds of H1N1pdm,
H3N2, and Vic with custom color scales for subclades within each subtype
and segment. These color scales match the scales used in the
nextflu-private builds, allowing us to include the public trees in our
monthly reports and easily switch between private and public trees
without changing color schemes across builds.

With this change, we can remove the "representative" builds from the
nextflu-private build config, since the public builds already provide
equal geographic and temporal sampling.

Closes #164
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huddlej committed Aug 30, 2024
1 parent c775b5a commit 101f5fe
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243 changes: 243 additions & 0 deletions config/h1n1pdm/ha/auspice_config.json
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{
"title": "Real-time tracking of influenza A/H1N1pdm evolution",
"maintainers": [
{
"name": "Jennifer Chang",
"url": "https://bedford.io/team/jennifer-chang/"
},
{
"name": "Jover Lee",
"url": "https://bedford.io/team/jover-lee/"
},
{
"name": "John Huddleston",
"url": "https://bedford.io/team/john-huddleston/"
},
{
"name": "Richard Neher",
"url": "https://neherlab.org/richard-neher.html"
},
{
"name": "Trevor Bedford",
"url": "https://bedford.io/team/trevor-bedford/"
}
],
"data_provenance": [
{
"name": "GISAID"
}
],
"build_url": "https://github.com/nextstrain/seasonal-flu",
"colorings": [
{
"key": "gt",
"title": "Genotype",
"type": "categorical"
},
{
"key": "num_date",
"title": "Date",
"type": "continuous"
},
{
"key": "clade_membership",
"title": "Clade",
"type": "categorical"
},
{
"key": "subclade",
"title": "Subclade",
"type": "categorical",
"scale": [
[
"C.1",
"#492AB5"
],
[
"C.1.1",
"#3F4CCB"
],
[
"C.1.2",
"#4271CE"
],
[
"C.1.5",
"#4C8FC0"
],
[
"C.1.7",
"#5AA5A8"
],
[
"C.1.7.1",
"#6DB38A"
],
[
"C.1.7.2",
"#85BA6F"
],
[
"C.1.8",
"#A0BE59"
],
[
"C.1.9",
"#BBBC49"
],
[
"D",
"#D2B340"
],
[
"D.1",
"#E19F3A"
],
[
"D.2",
"#E68033"
],
[
"D.3",
"#E2562B"
],
[
"D.4",
"#DB2823"
]
]
},
{
"key": "haplotype",
"title": "Derived haplotype",
"type": "categorical"
},
{
"key": "cTiter",
"title": "Antigenic advance (tree model)",
"type": "continuous"
},
{
"key": "cTiterSub",
"title": "Antigenic advance (sub model)",
"type": "continuous"
},
{
"key": "cTiter_x",
"title": "HI antigenic novelty",
"type": "continuous"
},
{
"key": "lbi",
"title": "Local branching index",
"type": "continuous"
},
{
"key": "ep",
"title": "Epitope mutations",
"type": "continuous"
},
{
"key": "ne",
"title": "Non-epitope mutations",
"type": "continuous"
},
{
"key": "glyc",
"title": "Glycosylation changes",
"type": "continuous"
},
{
"key": "region",
"title": "Region",
"type": "categorical"
},
{
"key": "country",
"title": "Country",
"type": "categorical"
},
{
"key": "division",
"title": "Division",
"type": "categorical"
},
{
"key": "accession_ha",
"title": "Accession (HA)",
"type": "categorical"
},
{
"key": "accession_na",
"title": "Accession (NA)",
"type": "categorical"
},
{
"key": "submitting_lab",
"title": "Submitting lab",
"type": "categorical"
},
{
"key": "originating_lab",
"title": "Originating lab",
"type": "categorical"
},
{
"key": "recency",
"title": "Submission date",
"type": "ordinal"
},
{
"key": "epiweek",
"title": "Epiweek (CDC)",
"type": "ordinal"
},
{
"key": "year_month",
"title": "Year/month",
"type": "categorical"
},
{
"key": "tsne_x",
"title": "t-SNE 1",
"type": "continuous"
},
{
"key": "tsne_y",
"title": "t-SNE 2",
"type": "continuous"
},
{
"key": "tsne_cluster",
"title": "t-SNE cluster",
"type": "categorical"
}
],
"geo_resolutions": [
"division",
"country",
"region"
],
"display_defaults": {
"map_triplicate": true,
"color_by": "clade_membership"
},
"filters": [
"clade_membership",
"subclade",
"region",
"country",
"division",
"submitting_lab",
"recency",
"epiweek",
"year_month",
"tsne_cluster"
],
"panels": [
"tree",
"map",
"entropy",
"frequencies"
]
}
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