seriation: bertinplot – R documentation

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bertinplot

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). bertin_cut_line() can be used to add cut lines (see Details).

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 or a matrix with colors 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`, `panel.blocks` and `panel.lines`. For circles and squares neg. values are represented by a dashed border. For blocks all blocks are the same size (can be used with `shading=TRUE`). `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). `shading` use gray shades to encode value instead of highlighting (default: FALSE). `shading.function` a function that accepts a single argument in range [.1, .8] and returns a valid corresponding color (e.g., using `rgb`). `frame` plot a grid to separate symbols (default: `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.

Cut lines can be added to an existing bertin plot using bertin_cut_line(x=NULL, y=NULL). x/y is can be a number indicating where to draw the cut line between two columns/rows. If both x and y is specified then one can select a row/column and the other can select a range to draw a line which does only span a part of the row/column. It is important to call bertinplot() with the option pop=FALSE.

Author(s)

Michael Hahsler

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.

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)

## some alternative displays
bertinplot(x, order, options = list(shading = TRUE, panel = panel.blocks))
bertinplot(x, order, options = list(panel = panel.lines))
bertinplot(x, order, options = list(panel = panel.squares))
bertinplot(x, order,
    options = list(panel = panel.circles, spacing = -0.5))

## plot with cut lines (we manually set the order here)
order <- ser_permutation(c(21, 16, 19, 18, 14, 12, 20, 15,
    17, 26, 13, 41,  7, 11, 5, 23, 28, 34, 31, 1, 38, 40,
    3, 39,  4, 27, 24,  8, 37, 36, 25, 30, 33, 35,  2,
    22, 32, 29, 10,  6,  9),
    c(4, 2, 1, 6, 8, 7, 5, 3))

bertinplot(x, order, options=list(pop=FALSE))
bertin_cut_line(,4) ## horizontal line between rows 4 and 5
bertin_cut_line(,7) ## separate "Right to Life" from the rest
bertin_cut_line(14,c(0,4)) ## separate a block of large values (vertically)

seriation

Infrastructure for Ordering Objects Using Seriation

v1.2-9

GPL-3

Authors

Michael Hahsler [aut, cre, cph], Christian Buchta [aut, cph], Kurt Hornik [aut, cph], Fionn Murtagh [ctb, cph], Michael Brusco [ctb, cph], Stephanie Stahl [ctb, cph], Hans-Friedrich Koehn [ctb, cph]

Initial release

2020-09-29