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add division level color-by feature

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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alliblk committed Jul 3, 2019
1 parent cfb01f9 commit 8fcea39d86cdee9a533501ccb2e9fd0559858f4d
Showing with 116 additions and 69 deletions.
  1. +45 −43 config/auspice_config.json
  2. +47 −2 config/colors.tsv
  3. +24 −24 data/publishable-zika-fauna-2018-10-15.fasta
@@ -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"
]
}
@@ -6,7 +6,7 @@ country american_samoa #b38752
country fiji #3F5ED0
country tonga #416CCE
country china #4379CD
country taiwan #4784C7
country taiwan #4784C7
country japan #4B8FC1
country italy #5098B9
country brazil #1e2c20
@@ -30,5 +30,50 @@ country puerto_rico #ca2c34
country jamaica #cf4148
country dominican_republic #d4565c
country haiti #d96b70
country cuba #df8085
country cuba #df8085
country usa #8862a3
division thailand #D3D3D3
division vietnam #D3D3D3
division singapore #D3D3D3
division french_polynesia #D3D3D3
division american_samoa #D3D3D3
division fiji #D3D3D3
division tonga #D3D3D3
division china #D3D3D3
division taiwan #D3D3D3
division japan #D3D3D3
division italy #D3D3D3
division brazil #D3D3D3
division peru #D3D3D3
division ecuador #D3D3D3
division colombia #D3D3D3
division french_guiana #D3D3D3
division suriname #D3D3D3
division venezuela #D3D3D3
division panama #D3D3D3
division nicaragua #D3D3D3
division honduras #D3D3D3
division el_salvador #D3D3D3
division guatemala #D3D3D3
division mexico #D3D3D3
division martinique #D3D3D3
division guadeloupe #D3D3D3
division saint_barthelemy #D3D3D3
division usvi #D3D3D3
division puerto_rico #D3D3D3
division jamaica #D3D3D3
division dominican_republic #D3D3D3
division haiti #D3D3D3
division cuba #D3D3D3
division usa #D3D3D3
division saint_croix #D3D3D3
division saint_john #D3D3D3
division saint_thomas #D3D3D3
division unknown #686868
division santander #fc4e2a
division tolima #feb24c
division cordoba #e31a1c
division valle_del_cauca #fed976
division atlantico #b10026
division risaralda #fd8d3c
division huila #ffffb2

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