Permutation Image Plot

Provides methods for plotting image plots for matrix and dist objects given a permutation. By default, no permutation is performed. This plot can also be used as a more versatile replacement of image plot in graphics based on grid.

pimage(x, order = NULL, col = NULL, main ="", xlab = "", ylab = "",
  axes = "auto", zlim=NULL, key=TRUE, key.lab="", symkey=TRUE,
  upper.tri = TRUE, lower.tri = TRUE, prop = NULL,
  ..., newpage=TRUE, pop=TRUE, gp=NULL)
a matrix or an object of class dist.
an object of class ser_permutation. If NULL the order in x is plotted.
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. For matrices containing negative values a symmetric diverging color palette is used.
plot title.
xlab, ylab
labels for the x and y axes.
a character string indicating if axes labels (column and row names of x) should be potted. Possible values are "auto" (only plot if less then 25 labels), "x", "y", "both" and "none".
vector with two elements giving the range (min, max) for representing the values in the matrix.
logical; add a color key? No key is available for logical matrices.
string plotted next to the color key.
logical; if x contains negative values, should the color palate be symmetric (zero is in the middle)>
upper.tri, lower.tri
a logical indicating whether to show the upper or lower triangle of the distance matrix.
logical; draw the cells in the image proportional (defaults to TRUE for dist and FALSE for 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).
a gpar object (see grid).

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.

The viewports used for plotting are called: "plot", "image" and "colorkey".

See Also

seriate, hmap, dissplot and image.

  • pimage
  • pimage.matrix
  • pimage.dist
x <- matrix(sample(c(FALSE, TRUE), 300, rep=TRUE), ncol=10,
  dimnames = list(1:30, LETTERS[1:10]))

## matrix (large values are dark/black)
pimage(x, main = "Random data", key = FALSE)

## plot seriated matrix (use red, proportional display and plot all axes)
pimage(x, seriate(x), col = c("white", "red"),
  prop = TRUE, axes="both", main = "Reordered data", key = FALSE)

## show correlation (for neg. values a diverging color scheme is
## used automatically)
pimage(cor(x), prop=TRUE)

## distances (note that low distances are represented dark!)
d <- dist(x, method = "binary")
pimage(d, upper.tri = FALSE, main = "Distances")

pimage(d, seriate(d), upper.tri = FALSE, main = "Distances", axes = "both")

## add to the plot using grid (use pop = FALSE)
pimage(x, pop = FALSE)
downViewport(name = "image")

## highlight cell 7/5 with a red arrow
grid.lines(x = c(5, 7), y = c(3, 5), arrow = arrow(),
  default.units = "native", gp = gpar(col="red", lwd = 3))

## add a red box around rows 15 and 16
grid.rect(x = 0.5, y = 15.5, width = ncol(x), height = 2,
  just = "left",
  default.units = "native", gp = gpar(col="red", lwd = 3, fill = NA))

## remove the viewports

## put several pimages on a page (uses viewports and newpage = FALSE)
pushViewport(viewport(layout=grid.layout(nrow = 1, ncol = 2)))
pushViewport(viewport(layout.pos.row = 1, layout.pos.col = 1))

## seriate matrix
o <- seriate(x)
pimage(x, o, main = "Random data", prop = TRUE, axes = "both", key = FALSE,
  newpage = FALSE)

pushViewport(viewport(layout.pos.row = 1, layout.pos.col = 2))

## add the reordered disimilarity matrix for rowa
pimage(d, o[[1]], upper.tri = FALSE, main = "Distances", axes = "both",
  key = FALSE, newpage = FALSE)

Documentation reproduced from package seriation, version 1.2-2, License: GPL-3

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