matrix_plot: Draws an image plot of a contact matrix with a legend strip...

In socialmixr: Social Mixing Matrices for Infectious Disease Modelling

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,
  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 minimium 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.
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.
...	further arguments to pass to image.plot()

Details

This is a function using the basic R graphics to make it easier for users of socialmixr to visualise social contact matrices.

Author(s)

Lander Willem

Examples

data(polymod)
mij <- contact_matrix(polymod, countries = "United Kingdom", age.limits = c(0, 18,65))$matrix
matrix_plot(mij)

socialmixr documentation built on Oct. 29, 2022, 1:09 a.m.