bertinplot {seriation}R Documentation

Plot a Bertin matrix

Description

Plot a data matrix of cases and variables. Each value is represented by a symbol. Large values are highlighted. The matrix can be rearranged to make structure in the data visible (see Falguerolles et al 1997).

Usage

bertinplot(x, order = NULL, highlight = TRUE,  options = NULL)   

Arguments

x a data matrix. Note that following Bertin, columns are variables and rows are cases. This behavior can be reversed using reverse = TRUE in options.
order an object of class ser_permutation to rearrange x before plotting. If NULL, no rearrangement is performed.
highlight a logical scalar indicating whether to use highlighting. If TRUE, all variables with values greater than the variable-wise mean are highlighted. To control highlighting, also a logical matrix with the same dimensions as x can be supplied.
options a list with options for plotting. The list can contain the following elements:
panel.function
a function to produce the symbols. Currently available functions are panel.bars (default), panel.circles, panel.squares and panel.lines.
reverse
logical indicating whether to swap cases and variables in the plot. The default (FALSE) is to plot cases as columns and variables as rows.
xlab, ylab
labels (default: use labels from x).
spacing
relative space between symbols (default: 0.2).
frame
plot a grid to separate symbols (default: code{FALSE}).
mar
margins (see par).
gp_labels
gpar object for labels (see gpar).
gp_panels
gpar object for panels (see gpar).
newpage
a logical indicating whether to start the plot on a new page (see grid.newpage).
pop
a logical indicating whether to pop the created viewports (see pop.viewport)?

Details

The plot is organized as a matrix of symbols. The symbols are drawn by a panel function, where all symbols of a row are drawn by one call of the function (using vectorization). The interface for the panel function is panel.myfunction(value, spacing, hl). value is the vector of values for a row scaled between 0 and 1, spacing contains the relative space between symbols and hl is a logical vector indicating which symbol should be highlighted.

References

de Falguerolles, A., Friedrich, F., Sawitzki, G. (1997): A Tribute to J. Bertin's Graphical Data Analysis. In: Proceedings of the SoftStat '97 (Advances in Statistical Software 6), 11–20.

See Also

ser_permutation, seriate, Package grid.

Examples

data("Irish")
scale_by_rank <- function(x) apply(x, 2, rank)
x <- scale_by_rank(Irish[,-6])

## use the the sum of absolute rank differences
order <- c(
  seriate(dist(x, "minkowski", p = 1)),
  seriate(dist(t(x), "minkowski", p = 1))
)

## plot
bertinplot(x, order)

## alternative display
bertinplot(x, order, 
    options = list(panel = panel.circles, spacing = -0.4))

[Package seriation version 0.1-4 Index]