Skip to content

Commit

Permalink
Update Auspice config for Nextclade tree
Browse files Browse the repository at this point in the history
This makes a few various updates to the Auspice config for the Nextclade tree including:
1. Making "clade_membership" default coloring. For this tree, we really care about MeV Genotype more than other colorings.
2. Call this "MeV Genotype (Nextstrain)". I think important to specify MeV Genotype to distinguish from the more common SNP-level genotype.
3. Clarify with "MeV Genotype (GenBank metadata)". The previous "(NCBI)" seemed like this could be a MeV Genotype call from an NCBI tool.
4. Order as Region then Country to follow ncov
5. Include clade_membership as filter option
  • Loading branch information
trvrb authored and kimandrews committed May 7, 2024
1 parent ba4c9be commit 07bf737
Showing 1 changed file with 13 additions and 11 deletions.
24 changes: 13 additions & 11 deletions nextclade/defaults/auspice_config.json
Original file line number Diff line number Diff line change
Expand Up @@ -17,41 +17,43 @@
"type": "continuous"
},
{
"key": "country",
"title": "Country",
"key": "clade_membership",
"title": "MeV Genotype (Nextstrain)",
"type": "categorical"
},
{
"key": "region",
"title": "Region",
"type": "categorical"
},
{
"key": "country",
"title": "Country",
"type": "categorical"
},
{
"key": "genotype_ncbi",
"title": "Genotype (NCBI)",
"title": "MeV Genotype (GenBank metadata)",
"type": "categorical"
},
{
"key": "is_reference",
"title": "WHO reference",
"title": "WHO Reference",
"type": "categorical"
},
{
"key": "clade_membership",
"title": "Genotype (augur clades)",
"type": "categorical"
}
],
"geo_resolutions": [
"country",
"region"
],
"display_defaults": {
"map_triplicate": true
"map_triplicate": true,
"color_by": "clade_membership"
},
"filters": [
"country",
"clade_membership",
"region",
"country",
"author"
],
"metadata_columns": [
Expand Down

0 comments on commit 07bf737

Please sign in to comment.