freyja plot

Create plot from AGG_RESULTS

freyja plot [OPTIONS] AGG_RESULTS

Options

--lineages

modify lineage breakdown

Default:

False

--times <times>

provide sample collection information,check data/times_metadata.csv for additional information

--interval <interval>

define whether the intervals are calculated daily D or monthly M use with –windowsize

Default:

MS

--config <config>

allows users to control the colors and grouping of lineages in the plot

--mincov <mincov>

min genome coverage included

Default:

60.0

--output <output>

specify output file name

Default:

mix_plot.pdf

--windowsize <windowsize>

width of the rolling average windowfor interval calculation

Default:

14

--lineageyml <lineageyml>

Custom lineage hierarchy file

--thresh <thresh>

pass a minimum lineage abundance

--writegrouped <writegrouped>

path to write grouped lineage data

--pathogen <pathogen>

Pathogen of interest.Not used if using –lineageyml option.

Default:

SARS-CoV-2

Options:

SARS-CoV-2 | MPXV | H5NX | H5NX-cattle | H1N1pdm | FLU-B-VIC | H3N2 | MEASLESN450 | MEASLES | RSVa | RSVb | DENV1 | DENV2 | DENV3 | DENV4

Arguments

AGG_RESULTS

Required argument

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Example Usage:

This resulting aggregated data can analyzed directly as a tsv file, or can be visualized using

freyja plot [aggregated-filename-tsv] --output [plot-filename(.pdf,.png,etc.)]

which provides a fractional abundance estimate for all aggregated samples. To provide a specific lineage breakdown, the --lineages flag can be used. We now provide a --config [path-to-plot-config-file] option that allows users to control the colors and grouping of lineages in the plot. The plot config file is a yaml file. More information about the plot config file can be found in the sample config file. Example outputs:

Summarized	Lineage-Specific

If users wish to include sample collection time information, this can be done using

freyja plot [aggregated-filename-tsv] --output [plot-filename(.pdf,.png,etc.)] --times [times_metadata.csv(note csv!)] --interval [MS or D (month/day bins)] --lineageyml [path-to-lineage.yml-file]

A custom lineage hierarchy file can be provided using --lineageyml option for visualization purposes. When using the --interval D option, the --windowsize NN should also be specified, where NN is the width of the rolling average window. See freyja/data/times_metadata.csv for an example collection time metadata file. Example outputs:

Month binning	Daily binning (with smoothing)