freyja dash

freyja dash [OPTIONS] AGG_RESULTS METADATA TITLE INTRO

Options

--thresh <thresh>

minimum lineage abundance

Default:

0.01

--headerColor <headercolor>

color of header

Default:

#2fdcf5

--bodyColor <bodycolor>

color of body

Default:

#ffffff

--scale_by_viral_load

scale by viral load

Default:

False

--nboots <nboots>

Number of Bootstrap iterations

Default:

1000

--serial_interval <serial_interval>

Serial Interval

Default:

5.5

--config <config>

control the colors and grouping of lineages in the plot

--mincov <mincov>

min genome coverage included

Default:

60.0

--output <output>

Output html file

Default:

mydashboard.html

--days <days>

specify number of days for growth calculation

Default:

56

--grthresh <grthresh>

minimum prevalence to calculate relative growth rate for

Default:

0.001

--lineageyml <lineageyml>

custom lineage hierarchy file

--keep_plot_files

keep the intermediate html for the core plot

Default:

False

Arguments

AGG_RESULTS

Required argument

METADATA

Required argument

TITLE

Required argument

INTRO

Required argument

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Example Usage:

We are now providing functionality to rapidly prepare a dashboard web page, directly from aggregated freyja output. This can be done with the command

freyja dash [aggregated-filename-tsv] [sample-metadata.csv] [dashboard-title.txt] [introContent.txt] --output [outputname.html] --lineage.yml [path-to-lineage.yml-file]

where the metadata file should have this form. See example title and intro-text files as well. For samples taken the same day, we average the freyja outputs by default. However, averaging can be performed that takes the viral loads into account using the --scale_by_viral_load flag. The header and body color can be changed with the --headerColor [mycolorname/hexcolor] and --bodyColor [mycolorname/hexcolor] option respectively. The --mincov option is also available, as in plot. The resulting dashboard will look like this.

The plot can now be configured using the --config [path-to-plot-config-file] option. The plot config file is a yaml file. More information about the plot config file can be found in the sample config file. By default, this will use the lineage hierarchy information present in freyja/dash/lineages.yml, but a custom hierarchy can be supplied using the --lineageyml [path-to-hierarchy-file] option. The --keep_plot_files option can be used keep the intermediate html for the core plot (will be deleted following incorporation into the main html output by default).

A CSV file will also be created along with the html dashboard which will contain the relative growth rates for each lineage. The lineages will be grouped together based on the Lineages key specified in the config file if provided.