CovInce

CovInce is an an application built in React for visualising numbers and proportions of lineages for cases of SARS-CoV2. It is currently used primarily for the spatiotemporal displays at https://covid19.sanger.ac.uk/ and https://covglobe.org/.

If you would like to deploy your own version of covince and need assistance please raise an issue and we will try to help.

Demo of the code in this repository (with old static data): http://covince.vercel.app

Configuration

Top-level sections

area_search_terms (optional) enable additional search terms for areas
chart [object]
- definitions [array] list of chart definitions
- settings [object] (optional)
chart_tooltip [object] [DEPRECATED - use chart.settings.tooltip]
- use_nomenclature [boolean] defaults to true
charts [array] list of chart definitions [DEPRECATED - use chart.definitions]
colors [object|array] (optional, static builds only) lineages mapped to color definitions, or a list of ordered colors. Optionally provide dark mode alternatives in the format { "light": "...", "dark": "..." }
datetime_format [string] for e.g. data updated date reference
dynamic_mode [object] (required for dynamic builds)
- initial_lineages [array|object] list of lineages, or an object mapping lineages to a numerical index in the colour palette. Numbers must be 0-8 for the built-in palette.
- colour_palette [array] (optional) list of color definitions or ordered colours. Optionally provide dark mode alternatives in the format { "light": "...", "dark": "..." }
- mutations ['single'|'multi'] (optional) enable mutation features, and whether multiple mutations can be selected
map [object]
- fade_uncertainty [{[parameter_id]: boolean}] (optional) enable fade uncertainty for specific parameters
- settings [object] (optional)
- viewport [object]
nomenclature [array] (optional) list of nomenclature definitions, the order will be reflected on the UI
ontology [object]
parameters [array] list of parameter definitions
timeline [object] (optional)

Area Search Terms

url [string] should load a JSON file with the following structure: { "search_term": "area_id", ... }
mode [string] type of search to apply to additional terms:
- padded-first-input-token pads the term to the length of the input and matches against the first token of the input padded to the original length

Chart settings

csv_download [boolean] (optional) defaults to true
tooltip [object] (optional)
- use_nomenclature [boolean] defaults to true
group_stacked_colors [boolean] (optional) reorder stacked areas to group colours together, defaults to true

Chart

allow_stack [boolean] (optional) enables stacking
default_type ['line'|'area']
heading [string]
parameter [string] should match a parameter id
preset ['percentage'] (optional) applies formatting rules [DEPRECATED - use parameter.format]
y_axis [object] (optional)

Chart Y-Axis

domain [number[]] (optional) reference
ticks [string[]] (optional) reference
reference_line [number] (optional) display a dotted line at the specified value
allow_data_overflow [boolean] (optional) reference

Map settings

default_lineage [string] (optional) should match a lineage in lists, defaults to first lineage
default_color_by [string] (optional) should match a parameter id, defaults to first parameter
default_color_scale ['linear'|'quadratic'|{[parameter_id]: 'linear'|'quadratic'}] (optional) can be a string for all parameters, or an object for specific parameters. Omit parameters from the object to hide the scale control.
color_map_domain [{[parameter_id]: object}] (optional) set the range of the colour map per parameter. Object should provide at least one of:
- min [number] (optional) minimum value of the color map
- max [number] (optional) maximum value of the color map

Map viewport

min_zoom [number] reference
default_lat [number] reference
default_lon [number] reference
default_zoom [number|object] reference provide a number for all screen types, or an object with properties: mobile, desktop, big
default_zoom_mob [number] Mobile option where proportions are different reference [DEPRECATED - use default_zoom.mobile]
bounds [object]
- min_longitude [number] reference
- max_longitude [number] reference
- min_latitude [number] reference
- max_latitude [number] reference

Nomenclature

lineage [string] should match a lineage in lists
alt_name [string] alternative name

Ontology

overview [object]
- category [string] e.g. "National Overview"
- heading [string] e.g. "England"
- short_heading [string] e.g. "National"
area [object]
- category [string] e.g. "Local authority"
- noun_plural [string] e.g. "local authorities"

Parameter

id [string]
display [string]
format ['percentage'] (optional) values should be 0-1 and are formatted as percentages
precision [number|object] (optional) decimal places for values, can a number for all values or an object with the following required keys:
- mean [number]
- range [number]

Timeline

label [string] (optional) e.g. "timeline",
initial_date [string] (optional) should be in ISO format e.g. "2021-01-01", defaults to latest date
date_format [string|object] (optional) can be a string for all dates or an object with the following required keys:
- heading [string] reference
- chart_tooltip [string] reference
frame_length [number] (optional) time in milliseconds per date when playing the timeline. Defaults to 100.