Map options (report options 6 and 7)

How to produce maps in the civet report

Mapping options

There are two types of mapping in civet:

  • Plot background diversity of lineages in the area of interest (report option 6)
  • Plot where your queries are (report option 7)

    • Both maps will show a default first view, but it is possible to alter that view by using the mouse wheel to zoom in and out, and by clicking and dragging on the map itself.

    Mapping queries (report option 6)

    This option allows you to plot queries on a map using their coordinates.

    Arguments:
    --query-map-file/-qmfile
    the underlying map file that the dots will be plotted on. Default: world map
    --latitude-column/-lat
    column in the metadata that contains latitude information for queries. Default: latitude
    --longitude-column/-long
    column in the metadata that contains longitude information for queries. Default: longitude


    Mapping background diversity (report option 7)

    This option summarises the Pango lineages as radial charts during a set time period at a specific geographical level. Only lineages that make up more than 5% of the overall sequence count are shown, with others shown under “other”.

    For more information on Pango lineages, see https://www.pango.network/

    Arguments:
    -bmfile--background-map-file
    the underlying map file that the radial charts will be displayed on.
    Default
    : world map
    --centroid-file
    file containing centroids of locations that lineages are summarised by, used to place radial plots on the map. Only necessary if a custom background map file is provided.
    -bmrange/--background-map-date-range
    Date range to restrict summary to. This can either be in terms of two dates (inclusive) in the format YYYY-MM-DD separated by a “:” (eg) or a single integer specifying the number of days either side of the date range of the queries. Eg --background-map-date-range 2020-09-10:2020-09-30 or --background-map-date-range 10
    Default
    : 2019-11-01 to present day
    -bmcol/--background-map-column
    column in the background dataset containing geographical information to summarise Pango lineages by. Must correspond to locations in the centroid file and background map file.
    Default
    : --location-column (country by default)
    --background-map-location/-bmloc
    comma separated list of locations to show background lineage diversity for. Must be valid locations matching the map file and the centroid file.
    Default
    : all valid locations in the background metadata file in the appropriate column.

    NB if the environment variable civet_mode is set to CLIMB, the default for the background-map-column is “suggested_adm2_grouping” instead, with the corresponding map and centroid files. This is an output of the COG-UK data processing pipeline, and is a version of the administrative level 2 (roughly county) of where the sequence was sampled. See https://github.com/COG-UK/docs/blob/master/geography_cleaning.md for more information.

    Next: Tree options