socialmixr (version 0.7.0)

matrix_plot: 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 (year)")

ylab

a title for the y axis (default: "Contact age group (year)")

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.

Author

Lander Willem

Details

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

Examples

if (FALSE) {
data(polymod)
mij <- contact_matrix(
  polymod,
  countries = "United Kingdom",
  age_limits = c(0, 18, 65)
)$matrix
matrix_plot(mij)
}