Draws an image plot of a contact matrix with a legend strip and the numeric values in the cells.
Source:R/matrix_plot.R
matrix_plot.Rd
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 aretopo.colors()
,terrain.colors()
andhcl.colors()
. User-defined functions are also possible if they take the number of colors to be in the palette as function argument.
Examples
if (FALSE) { # \dontrun{
data(polymod)
mij <- contact_matrix(polymod, countries = "United Kingdom", age.limits = c(0, 18, 65))$matrix
matrix_plot(mij)
} # }