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To do a bit more analysis at the within-colombia level, I wanted to add a color-by feature to the nextstrain build that would allow us to look at which department within Colombia a genome was sampled from. This required adding this information to the input data, altering the auspice_config to add a color by division flag, and adding the colors that I want to the colors.tsv file.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,45 @@ | ||
| { | ||
| "title": "Real-time tracking of Zika virus evolution", | ||
| "color_options": { | ||
| "gt": { | ||
| "menuItem": "genotype", | ||
| "legendTitle": "Genotype", | ||
| "type": "discrete", | ||
| "key": "genotype" | ||
| }, | ||
| "num_date": { | ||
| "menuItem": "date", | ||
| "legendTitle": "Sampling date", | ||
| "type": "continuous", | ||
| "key": "num_date" | ||
| }, | ||
| "authors": { | ||
| "key":"authors", | ||
| "legendTitle":"Authors", | ||
| "menuItem":"authors", | ||
| "type":"discrete" | ||
| }, | ||
| "country": { | ||
| }, | ||
| "region": { | ||
| } | ||
| }, | ||
| "geo": [ | ||
| "country", | ||
| "region" | ||
| ], | ||
| "defaults": { | ||
| "mapTriplicate": true | ||
| }, | ||
| "maintainer": [ | ||
| "Alli Black", | ||
| "https://bedford.io/team/allison-black/" | ||
| ], | ||
| "filters": [ | ||
| "country", | ||
| "region", | ||
| "authors" | ||
| ] | ||
| } | ||
| { | ||
| "title": "Real-time tracking of Zika virus evolution", | ||
| "color_options": { | ||
| "gt": { | ||
| "menuItem": "genotype", | ||
| "legendTitle": "Genotype", | ||
| "type": "discrete", | ||
| "key": "genotype" | ||
| }, | ||
| "num_date": { | ||
| "menuItem": "date", | ||
| "legendTitle": "Sampling date", | ||
| "type": "continuous", | ||
| "key": "num_date" | ||
| }, | ||
| "authors": { | ||
| "key":"authors", | ||
| "legendTitle":"Authors", | ||
| "menuItem":"authors", | ||
| "type":"discrete" | ||
| }, | ||
| "country": { | ||
| }, | ||
| "region": { | ||
| }, | ||
| "division": { | ||
| } | ||
| }, | ||
| "geo": [ | ||
| "country", | ||
| "region" | ||
| ], | ||
| "defaults": { | ||
| "mapTriplicate": true | ||
| }, | ||
| "maintainer": [ | ||
| "Alli Black", | ||
| "https://bedford.io/team/allison-black/" | ||
| ], | ||
| "filters": [ | ||
| "country", | ||
| "region", | ||
| "authors" | ||
| ] | ||
| } |
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