This project is maintained by nextstrain
Just as we can specify a build-specific analysis options in the builds.yaml
file, we can also specify build-specific visualization options in this directory.
Looking at the builds.yaml
file, the last few lines are:
files:
auspice_config: "my_profiles/example/my_auspice_config.json"
This points to a JSON file that parameterizes the output files used for visualizion with Auspice. Let's look at what kinds of customization options we can use this for.
If you'd like to specify a custom color scale, you can add a colors.tsv
file, where each line is a tab-delimited list of a metadata column name; a metadata value; and a corresponding hex code.
The first few lines of the example file look like this:
country Russia #5E1D9D
country Serbia #4D22AD
country Europe #4530BB
...
Make sure to also add
files:
colors: "my_profiles/<name>/colors.tsv"
to your builds.yaml
file.
The dataset description, which appears below the visualizations, is read from a file which is specified in builds.yaml
. Per-build description can be set by specifying them in the build.
builds:
north-america: # name of the build; this can be anything
description: my_profiles/example/north-america-description.md
If that is not provided, then a per-run description is used, also specified in builds.yaml
:
files:
description: my_profiles/example/my_description.md
metadata.tsv
my_profiles/<name>/auspice_config.json
colorings
block of this JSON:...
"colorings": [
{
"key": "location",
"title": "Location",
"type": "categorical"
},
{
"key": "metadata_column_name",
"title": "Display name for interface",
"type": "categorical" or "continuous"
}
...
]
...
You can specify the default view in the display_defaults
block of an auspice_config.json
file (see above)
...
"display_defaults": {
"color_by": "division",
"distance_measure": "num_date",
"geo_resolution": "division",
"map_triplicate": true,
"branch_label": "none"
},
...
Similarly, you can choose which panels to enable in the panels
block:
...
"panels": [
"tree",
"map",
"entropy"
]
...