matrix_plot: Draws an image plot of a contact matrix with a legend strip...
In socialmixr: Social Mixing Matrices for Infectious Disease Modelling

matrix_plot

R Documentation

Draws an image plot of a contact matrix with a legend strip and the numeric values in the cells.

Description

This function combines the R image.plot function with numeric contact rates in the matrix cells.

Usage

matrix_plot(
  mij,
  min.legend = 0,
  max.legend = NA,
  num.digits = 2,
  num.colors = 50,
  main,
  xlab,
  ylab,
  legend.width,
  legend.mar,
  legend.shrink,
  cex.lab,
  cex.axis,
  cex.text,
  color.palette = heat.colors
)

Arguments

`mij`	a contact matrix containing contact rates between participants of age i (rows) with contacts of age j (columns). This is the default matrix format of `contact_matrix()`.
`min.legend`	the color scale minimum (default = 0). Set to NA to use the minimum value of `mij`.
`max.legend`	the color scale maximum (default = NA). Set to NA to use the maximum value of `mij`.
`num.digits`	the number of digits when rounding the contact rates (default = 2). Use NA to disable this.
`num.colors`	the number of color breaks (default = 50)
`main`	the figure title
`xlab`	a title for the x axis (default: "Age group (years)")
`ylab`	a title for the y axis (default: "Contact age group (years)")
`legend.width`	width of the legend strip in characters. Default is 1.
`legend.mar`	width in characters of legend margin. Default is 5.1.
`legend.shrink`	amount to shrink the size of legend relative to the full height or width of the plot. Default is 0.9.
`cex.lab`	size of the x and y labels (default: 1.2)
`cex.axis`	size of the axis labels (default: 0.8)
`cex.text`	size of the numeric values in the matrix (default: 1)
`color.palette`	the color palette to use (default: `heat.colors()`). Other examples are `topo.colors()`, `terrain.colors()` and `hcl.colors()`. User-defined functions are also possible if they take the number of colors to be in the palette as function argument.

Details

This is a function using basic R graphics to visualise a social contact matrix.

Author(s)

Lander Willem

Examples

## Not run: 
data(polymod)
mij <- contact_matrix(polymod, countries = "United Kingdom", age.limits = c(0, 18, 65))$matrix
matrix_plot(mij)

## End(Not run)

socialmixr documentation built on Oct. 18, 2024, 5:14 p.m.