Customizing visualization

Visualization options can be configured in either a workflow config file or a Auspice config file, depending on the option.

Options in the workflow config file

These options can be coded into the workflow config file directly without requiring a custom Auspice config file.

Custom color schemes

To specify a custom color scale:

  1. 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. Example:

    country Russia  #5E1D9D
    country Serbia  #4D22AD
    country Europe  #4530BB
  2. Update your workflow config file with a reference:

      colors: "my-ncov-analyses/colors.tsv"

Changing the dataset description

The dataset description, which appears below the visualizations, is read from a file which is specified in the workflow config file. Per-build description can be set by specifying them in the workflow config file:

  north-america: # name of the build
    description: my-ncov-analyses/

If that is not provided, then a per-run description is used, also specified in the workflow config file:

  description: my-ncov-analyses/

Options in the Auspice config file

These options require creating an Auspice config file, used to configure Auspice. It is specified in the workflow config file using the auspice_config entry. Example:

auspice_config: ncov-tutorial/auspice-config-custom-data.json

This overrides the default Auspice config file, defaults/auspice_config.json.

Adding custom metadata fields to color by

  1. Add a valid metadata column to your metadata.tsv

  2. Add an entry to the colorings block of the Auspice config file:

    "colorings": [
       "key": "location",
       "title": "Location",
       "type": "categorical"
       "key": "metadata_column_name",
       "title": "Display name for interface",
       "type": "<categorical/continuous>"

Choosing defaults

You can specify the default view in the display_defaults block of an Auspice config file:

"display_defaults": {
  "color_by": "division",
  "distance_measure": "num_date",
  "geo_resolution": "division",
  "map_triplicate": true,
  "branch_label": "none"

Choosing panels to display

Similarly, you can choose which panels to enable in the panels block:

"panels": [