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
- --pathogen <pathogen>
Pathogen of interest.Not used if using –lineageyml option.
- Default:
SARS-CoV-2- Options:
SARS-CoV-2 | MPXV | H5NX | H1N1pdm | FLU-B-VIC | MEASLESN450 | MEASLES | RSVa | RSVb
Arguments
- AGG_RESULTS
Required argument
- METADATA
Required argument
- TITLE
Required argument
- INTRO
Required argument
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.