Heatmap

Plots a heatmap.

Usage

plot_heatmap(object, ...)

# S4 method for matrix
plot_heatmap(object, diag = TRUE, upper = TRUE, lower = TRUE, freq = FALSE)

# S4 method for data.frame
plot_heatmap(object, diag = TRUE, upper = TRUE, lower = TRUE, freq = FALSE)

# S4 method for dist
plot_heatmap(object, diag = FALSE, upper = FALSE, lower = !upper)

Arguments

object

A \(m \times p\) numeric matrix or data.frame of count data (absolute frequencies giving the number of individuals for each class).

...

Currently not used.

diag

A logical scalar indicating whether the diagonal of the matrix should be plotted. Only used if object is a symmetric matrix.

upper

A logical scalar indicating whether the upper triangle of the matrix should be plotted. Only used if object is a symmetric matrix.

lower

A logical scalar indicating whether the lower triangle of the matrix should be plotted. Only used if object is a symmetric matrix.

freq

A logical scalar indicating whether relative frequency should be used instead of counts (absolute frequency).

Value

A ggplot2::ggplot object.

References

Desachy, B. (2004). Le sériographe EPPM: un outil informatisé de sériation graphique pour tableaux de comptages. Revue archéologique de Picardie, 3(1), 39-56. doi:10.3406/pica.2004.2396 .

See also

pvi()

Other plot methods: plot_bar, plot_diversity, plot_line, plot_spot()

Author

N. Frerebeau

Examples

## Abundance data (data from Desachy 2004)
data("compiegne", package = "folio")

## Plot matrix diagram...
plot_heatmap(compiegne)

plot_heatmap(compiegne, freq = TRUE)


## Presence/absence data
inc <- sample(0:1, size = 100, replace = TRUE)
bin <- matrix(data = as.logical(inc), nrow = 10, ncol = 10)

plot_heatmap(bin) +
  ggplot2::scale_fill_manual(values = c("TRUE" = "black", "FALSE" = "white"))