Plots a spot matrix.

plot_spot(object, ...)

# S4 method for matrix
plot_spot(object, threshold = NULL, diag = TRUE, upper = TRUE, ...)

# S4 method for dist
plot_spot(object, diag = FALSE, upper = FALSE, ...)

# S4 method for OccurrenceMatrix
plot_spot(object, diag = FALSE, upper = FALSE, ...)

Arguments

object

An abundance matrix to be plotted.

...

Extra parameters to be passed to threshold.

threshold

A function that takes a numeric vector as argument and returns a numeric threshold value. If NULL (the default), no threshold is computed.

diag

A logical scalar indicating whether the diagonal of the matrix should be plotted.

upper

A logical scalar indicating whether the upper triangle of the matrix should be plotted.

Value

A ggplot object.

Details

The spot matrix can be considered as a variant of the Bertin diagram where the data are first transformed to relative frequencies.

Note

Adapted from Dan Gopstein's original idea. Credit should be given to him.

See also

Author

N. Frerebeau

Examples

## Plot spot diagram of count data... data("mississippi", package = "folio") counts <- as_count(mississippi) ### ...without threshod plot_spot(counts)
### ...with the column means as threshold plot_spot(counts, threshold = mean)
### ...with the column medians as threshold plot_spot(counts, threshold = median)