Auspice uses a number of default color schemes to color the tree using meta data or values that the augur pipeline computed. In some cases these defaults are not suitable for particular type of data (countries, host species often fall into this category) and it is advisable to specify your own color schemes. To specify a mapping between discrete values and colors, you can pass a tab-delimited fill to the augur export step. This file should contain 3 columns separated by tab characters. The first columns specifies the trait (e.g.~country, host species, ...), the second columns specifies the value of the trait, and the third the associated color in hexadecimal notation.
country thailand #511EA8 country vietnam #4928B4 country singapore #4334BF country french_polynesia #4041C7 country american_samoa #3F50CC country fiji #3F5ED0 [...]
The hexadecimal notation starts with a #, followed by two letters coding for red, green, blue values. If you need advice or inspiration for colors, have a look at colorbrewer. In our zika tutorial, this color file will be passed to the augur export command as
Latitudes and longitudes
To place sequences on a map, auspice needs to know where the locations you specify are on the globe. These coordinates are provided by augur and augur has preset coordinates for many places. Some places, however, will inevitably be missing and you need to tell augur the latitudes and longitude of all locations not covered by defaults. The file for latitude and longitude needs to be a tab-delimited table with four columns:
country brazil -10.3333332 -53.1999999 country colombia 2.893108 -73.7845142 country dominican_republic 18.50012 -69.98857 country ecuador -1.3397667 -79.3666964 country french_polynesia -17.6797 -149.4068 country guatemala 15.6356088 -89.8988086 [...]
The first columns specifies the type of location (country, city, region, ...) corresponding to a field in your meta data. The second is the actual name of the location, while the third and fourth columns are latitude and longitude.