Customizing visualization
Visualization options can be configured in either a workflow config file or a Auspice config file, depending on the option.
Table of Contents
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:
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 ...
Update your workflow config file with a reference:
files: 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:
builds:
north-america: # name of the build
description: my-ncov-analyses/north-america-description.md
If that is not provided, then a per-run description is used, also specified in the workflow config file:
files:
description: my-ncov-analyses/my_description.md
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
Add a valid metadata column to your
metadata.tsv
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": [
"tree",
"map",
"entropy"
]