Report content and report preset options

Each element of the civet report is associated with a number:

1. Tables describing the queries. (See Table options)
2. Summarise the phylogenetic context of the queries in table form. (See Table options)
3. Show phylogenetic trees of the queries and their surrounding phylogenetic context, known as "catchments". (See Tree options)
4. Show "snpit" plot of each catchment, which visualises the SNPs found in each query sequence compared to the reference sequence.
5. Produces timelines of queries per catchment (See Timeline options)
6. Summarises Pango lineages found in the background dataset at appropriate geographical level (eg country) and displays them on a map. (See Map options)
7. Plots queries as dots on a map (See Map options)

Provide combinations of these letters as a comma separated string to define the elements present in the report.

You can also use presets report configuration using -rp/--report-preset:

hold_the_sauce: 1,2 (just summary tables, no figures)

the_usual : 1,2,3,4,5 (All figures except maps)

the_works : 1,2,3,4,5,7 (All figures except background diversity map)

the_whole_shebang : 1,2,3,4,5,6,7 (everything!)

Default:
the usual (1,2,3,4,5)

Usage:
--report-content {$LIST} or -rc {$LIST}
--report-preset {$PRESET} or -rp {$PRESET}

Report title

Title to show at the top of the report.

Default:
civet report

Usage:
--report-title {$TITLE} or -rt {$TITLE}

Colour theme

Report theme colour, specifiy a HEX colour code to colour the panels and highlighting in the report.

Default:
#7178bc

Usage:
-ct/--colour-theme {$HEX_CODE}

Colour map

Comma separated string of HEX codes or HTML-support names to colour factors in different figures in the report by.

Default:
civet logo colours

Usage:
--colour-map/-cmap {$LIST}

Anonymise

Provides anonymised IDs to replace sequence names for display in the report.

Alternatively, you may provide a column in the metadata to refer to queries by using -rcol/--report-column. See Input column configuration

Default:
False

Usage:
--anonymise