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A ggplot scale for pneumococcal serotypes that keeps PCV groups together

Source: R/utils-serotype-scales.R
scale_fill_serotype.Rd

The scale groups colours by PCV group, but it is important to have the source data using the same levels as this scale otherwise the colour legend will be ordered in a different sequence. This can be achieved using relevel_serotypes,

Usage

scale_fill_serotype(
  ...,
  palette_fn = scales::brewer_pal(palette = "Dark2"),
  undefined = "#606060",
  exprs = rlang::exprs()
)

Arguments

...

an unwrapped version of the exprs parameter Named arguments passed on to ggplot2::scale_fill_manual

values

a set of aesthetic values to map data values to. The values will be matched in order (usually alphabetical) with the limits of the scale, or with breaks if provided. If this is a named vector, then the values will be matched based on the names instead. Data values that don't match will be given na.value.

aesthetics

Character string or vector of character strings listing the name(s) of the aesthetic(s) that this scale works with. This can be useful, for example, to apply colour settings to the colour and fill aesthetics at the same time, via aesthetics = c("colour", "fill").

breaks

One of:

  • NULL for no breaks

  • waiver() for the default breaks (the scale limits)

  • A character vector of breaks

  • A function that takes the limits as input and returns breaks as output

na.value

The aesthetic value to use for missing (NA) values

palette_fn

a function that returns a set of colours for a number of levels. Such functions can be obtained from things like scales::brewer_pal(...)

undefined

the colour for the last group which is assumed to be the Unknown types

exprs

a list of formulae with a predicate on the LHS and a PCV group name on the RHS. which are interpreted as the parameters for a dplyr::case_when call. This must be protected against interpretation by wrapping it in rlang::exprs(). The predicates are tested against avoncap::serotype_data$map and could use any of the following columns 'serotype', 'PCV7', 'PCV13', 'PCV15', 'PCV20', 'PPV23', 'PCV13on7', 'PCV15on13', 'PCV20on15', 'PPV23on20', 'PCV10SSI', 'PCV10GSK', 'PCV15Zhifei', 'PCV24Vaxcyte', 'PCV24Affinivax' a default option of the form TRUE ~ "Non PCV serotype" must exist to capture unmatched items.

Value

A ggplot2 scale