augur measurements

Create JSON files suitable for visualization within the measurements panel of Auspice.

usage: augur measurements [-h] {export,concat} ...

Positional Arguments

subcommand

Possible choices: export, concat

Sub-commands

export

Export a measurements JSON for a single collection

augur measurements export [-h] --collection TSV
                          [--strain-column STRAIN_COLUMN]
                          [--value-column VALUE_COLUMN] --output-json JSON
                          [--collection-config JSON]
                          [--grouping-column GROUPING_COLUMN [GROUPING_COLUMN ...]]
                          [--key KEY] [--title TITLE]
                          [--x-axis-label X_AXIS_LABEL]
                          [--thresholds THRESHOLDS [THRESHOLDS ...]]
                          [--filters FILTERS [FILTERS ...]]
                          [--group-by GROUP_BY]
                          [--measurements-display {raw,mean}]
                          [--show-overall-mean] [--show-threshold]
                          [--include-columns INCLUDE_COLUMNS [INCLUDE_COLUMNS ...]]
                          [--minify-json]

REQUIRED

--collection

Collection of measurements and metadata in a TSV file. Keep in mind duplicate columns will be renamed as ‘X’, ‘X.1’, ‘X.2’…’X.N’

--strain-column

Name of the column containing strain names. Provided column will be renamed to strain so please make sure no other columns are named strain. Strain names in this column should match the strain names in the corresponding Auspice dataset JSON. (default: ‘strain’)

Default: 'strain'

--value-column

Name of the column containing the numeric values to be plotted for the given collection. Provided column will be renamed to value so please make sure no other columns are named value. (default: ‘value’)

Default: 'value'

--output-json

Output JSON file. The file name must follow the Auspice sidecar file naming convention to be recognized as a sidecar file. See Nextstrain data format docs for more details.

COLLECTION CONFIGURATION

These options control the configuration of the collection for Auspice. You can provide a config JSON (which includes all available options) or command line arguments (which are more limited). Command line arguments will override the values set in the config JSON.

--collection-config

Collection configuration file for advanced configurations.

--grouping-column

Name of the column(s) that should be used as grouping(s) for measurements. Note that if groupings are provided via command line args, the default group-by field in the config JSON will be dropped.

--key

A short key name of the collection for internal use within Auspice. If not provided via config or command line option, the collection TSV filename will be used.

--title

The full title of the collection to display in the measurements panel title. If not provided via config or command line option, the panel’s default title is ‘Measurements’.

--x-axis-label

The short label to display for the x-axis that describles the value of the measurements. If not provided via config or command line option, the panel’s default x-axis label is ‘measurement values’.

--thresholds

Measurements value threshold(s) to be displayed in the measurements panel.

--filters

The columns that are to be used a filters for measurements. If not provided, all columns will be available as filters.

--group-by

The default grouping column. If not provided, the first grouping will be used.

--measurements-display

Possible choices: raw, mean

The default display of the measurements

--show-overall-mean, --hide-overall-mean

Show or hide the overall mean per group by default

--show-threshold, --hide-threshold

Show or hide the threshold(s) by default. This will be ignored if no threshold(s) are provided.

OPTIONAL SETTINGS

--include-columns

The columns to include from the collection TSV in the measurements JSON. Be sure to list columns that are used as groupings and/or filters. If no columns are provided, then all columns will be included by default.

--minify-json

Export JSON without indentation or line returns.

Default: False

concat

Concatenate multiple measurements JSONs into a single JSON file

augur measurements concat [-h] --jsons JSONs [JSONs ...] --output-json JSON
                          [--default-collection DEFAULT_COLLECTION]
                          [--minify-json]

REQUIRED

--jsons

Measurement JSON files to concatenate.

--output-json

Output JSON file

OPTIONAL SETTINGS

--default-collection

The key of the default collection to display. If not provided, the first collection of the first JSON file will be displayed

--minify-json

Concatenate JSONs without indentation or line returns.

Default: False