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Add segment-specific Auspice configs for 2y builds
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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{ | ||
"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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