Heatmap

Plots a heatmap.

Usage

plot_heatmap(object, ...)

# S4 method for class 'matrix'
plot_heatmap(
  object,
  color = NULL,
  diag = TRUE,
  upper = TRUE,
  lower = TRUE,
  freq = FALSE,
  margin = 1,
  fixed_ratio = TRUE,
  axes = TRUE,
  legend = TRUE,
  ...
)

# S4 method for class 'data.frame'
plot_heatmap(
  object,
  color = NULL,
  diag = TRUE,
  upper = TRUE,
  lower = TRUE,
  freq = FALSE,
  margin = 1,
  fixed_ratio = TRUE,
  axes = TRUE,
  legend = TRUE,
  ...
)

# S4 method for class 'dist'
plot_heatmap(
  object,
  color = NULL,
  diag = FALSE,
  upper = FALSE,
  lower = !upper,
  axes = TRUE,
  legend = TRUE,
  ...
)

Arguments

object

A \(m \times p\) numeric matrix or data.frame of count data (absolute frequencies giving the number of individuals for each category, i.e. a contingency table).

...

Currently not used.

color

A vector of colors or a function that when called with a single argument (an integer specifying the number of colors) returns a vector of colors.

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 conditional proportions given margins should be used (i.e. entries of object, divided by the appropriate marginal sums).

margin

An integer vector giving the margins to split by: 1 indicates individuals/rows (the default), 2 indicates variables/columns. Only used if freq is TRUE.

fixed_ratio

A logical scalar: should a fixed aspect ratio (1) be used?

axes

A logical scalar: should axes be drawn on the plot? It will omit labels where they would abut or overlap previously drawn labels.

legend

A logical scalar: should a legend be displayed?

Value

plot_heatmap() is called for its side-effects: it results in a graphic being displayed (invisibly returns object).

See also

Other plot methods: matrigraph(), plot_bertin(), plot_diceleraas(), plot_ford(), plot_rank(), plot_spot(), seriograph()

Author

N. Frerebeau

Examples

## Data from Lipo et al. 2015
data("mississippi", package = "folio")

## Plot raw data
plot_heatmap(mississippi)


## Change colors
plot_heatmap(mississippi, color = color("iridescent"))


## Plot conditional proportions
plot_heatmap(mississippi, freq = TRUE, margin = 1)

plot_heatmap(mississippi, freq = TRUE, margin = 2)