plot.incidence2: Plot an incidence object
In incidence2: Compute, Handle and Plot Incidence of Dated Events

plot.incidence2

R Documentation

Plot an incidence object

Description

plot() can be used to provide a bar plot of an incidence object. Due to the complexities with automating plotting it is some what experimental in nature and we recommend calling ggplot2 but this function is often sufficient for generating a quick visualisation of an ⁠<incidence2>⁠ object.

Usage

## S3 method for class 'incidence2'
plot(
  x,
  y,
  width = 1,
  colour_palette = vibrant,
  border_colour = NA,
  na_colour = "grey",
  alpha = 0.7,
  fill = NULL,
  legend = c("right", "left", "bottom", "top", "none"),
  title = NULL,
  angle = 0,
  size = NULL,
  nrow = NULL,
  n_breaks = 6L,
  show_cases = FALSE,
  ...
)

Arguments

`x`	`⁠<incidence2>⁠` object.
`y`	Not used. Required for compatibility with the `plot()` generic.
`width`	`⁠[numeric]⁠` Value between 0 and 1 indicating the relative size of the bars to the interval. Default 1.
`colour_palette`	`⁠[function]⁠` The color palette to be used for the different count variables. Defaults to `vibrant` (see `?palettes`).
`border_colour`	`⁠[character]⁠` The color to be used for the borders of the bars. Use `NA` (default) for invisible borders.
`na_colour`	`⁠[character]⁠` The colour to plot `NA` values in graphs. Defaults to `grey`.
`alpha`	`⁠[numeric]⁠` The alpha level for color transparency, with 1 being fully opaque and 0 fully transparent Defaults to 0.7.
`fill`	`⁠[character]⁠` Which variable to colour plots by. Must be a `group` or `count` variable and will mean that variable is not used for facetting. If NULL no distinction if made for plot colours.
`legend`	`⁠[character]⁠` Position of legend in plot. Only applied if `fill` is not NULL. One of "right" (default), "left", "bottom", "top" or "none".
`title`	`⁠[character]⁠` Optional title for the graph.
`angle`	`⁠[numeric]⁠` Rotation angle for text.
`size`	`⁠[numeric]⁠` text size in pts.
`nrow`	`⁠[integer]⁠` Number of rows used for facetting if there are group variables present and just one count in the incidence object. Numeric values are coerced to integer via `as.integer()`.
`n_breaks`	`⁠[integer]⁠` Approximate number of breaks calculated using `scales::breaks_pretty`. Numeric values are coerced to integer via `as.integer()`. Default 6L.
`show_cases`	`⁠[logical]⁠` if `TRUE`, then each observation will be shown individually in a square format. Normally only used for outbreaks with a small number of cases. Defaults to `FALSE`.
`...`	Not currently used.

Details

Facetting will occur automatically if either grouping variables or multiple counts are present.
If there are multiple count variables, each count will occupy a different row of the resulting plot.
Utilises ggplot2 so this must be installed to use.