R: Permutation image plot

pimage {seriation}

R Documentation

Permutation image plot

Description

Provides methods for plotting image plots for matrix and dist objects given a permutation.

Usage

pimage(x, order = NULL, col = NULL, main ="", xlab = "", ylab = "", axes = TRUE, ..., newpage=TRUE, pop=TRUE)

## S3 method for class 'matrix'
pimage(x, order=NULL, col=NULL, main="", xlab="", ylab="",
        axes=TRUE, ..., newpage=TRUE, pop=TRUE)
## S3 method for class 'dist'
pimage(x, order = NULL, col = NULL, main="", xlab="", ylab="",
        axes = TRUE, upper.tri = TRUE, lower.tri = TRUE, ...,
	        newpage=TRUE, pop=TRUE)

Arguments

`x`	a matrix or an object of class `dist`.
`order`	an object of class `ser_permutation`. If `NULL` the order in `x` is plotted.
`col`	a list of colors used. If `NULL`, a gray scale is used (for matrix larger values are displayed darker and for `dist` smaller distances are darker). For matrices containing logical data, black and white is used.
`main`	Plot title.
`xlab, ylab`	labels for the x and y axes.
`axes`	a logical indicating whether to add axes using the labels of `x`. The default value (`TRUE`) shows only axes if the dimension is below 10 (so it is reasonable to show labels).
`upper.tri, lower.tri`	a logical indicating whether to show the upper or lower triangle of the distance matrix.
`...`	further arguments passed on to `image` in graphics.
`newpage, pop`	two logical. Start plot on a new page and pop the viewports after plotting (see Grid).

Details

Plots a matrix in its original row and column orientation. This means, in a plot the columns become the x-coordinates and the reversed rows the y-coordinates.

If x is of class dist it is converted to full-storage representation before plotting.

Author(s)

Christian Buchta and Michael Hahsler

Examples

x <- matrix(sample(c(FALSE, TRUE), 150, rep=TRUE), ncol=10)

## matrix
pimage(x, main = "random data")

## plot seriated matrix
pimage(x, seriate(x), col = c("white", "green"), main = "reordered data")

## distances
d <- dist(x, method = "binary")
pimage(d, lower.tri = FALSE)

pimage(d, seriate(d), lower.tri = FALSE)

[Package seriation version 1.0-6 Index]