image2: Improved image() function

In LICORS: Light Cone Reconstruction of States - Predictive State Estimation From Spatio-Temporal Data

Description

Improved version of the image function in the graphics package. In particular, it displays matrices the way they are shown in the R console, not transposed/rearranged/... For example, a covariance matrix has the diagonal in from top-left to bottom-right as it should be, and not from bottom-left to top-right.

The function make_legend also provides a better color scale legend handling.

Optionally image2 displays a color histogram below the image, which can be used to refine the display of a matrix by trimming outliers (as they can often distort the color representation).

Usage

image2(x = NULL, y = NULL, z = NULL, col = NULL, axes = FALSE, legend = TRUE, 
    xlab = "", ylab = "", zlim = NULL, density = FALSE, max.height = NULL, 
    zlim.label = "color scale", ...)

make_legend(data = NULL, col = NULL, side = 1, zlim = NULL, col.ticks = NULL, 
    cex.axis = 2, max.height = 1, col.label = "")

Arguments

x,y	locations of grid lines at which the values in z are measured. These must be finite, non-missing and in (strictly) ascending order. By default, equally spaced values from 0 to 1 are used. If x is a list, its components x$x and x$y are used for x and y, respectively. If the list has component z this is used for z.
z	a matrix containing the values to be plotted (NAs are allowed). Note that x can be used instead of z for convenience.
col	colors: either a string decribing a pallette from the RColorBrewer package (see also http://colorbrewer2.org/), or a list of colors (see image for suggestions).
axes	a logical value indicating whether both axes should be drawn on the plot.
xlab	a label for the x axis
ylab	a label for the y axis
legend	logical; if TRUE a color legend for will be plotted
zlim	minimum and maximum z values for which colors should be plotted, defaulting to the range of the finite values of z.
zlim.label	character string (default: "color scale") to write next to the color legend
density	logical; if TRUE a color histogram (density) will be plotted. Default: FALSE.
max.height	height of the density plot (typically not modified by user)
...	optional arguments passed to image
data	data for which the legend should be plotted
side	on which side of the plot (1=bottom, 2=left, 3=top, 4=right)
col.ticks	color tick marks
cex.axis	The magnification to be used for axis annotation relative to the current setting of cex.
col.label	same as zlim.label

See Also

image, image.plot

Examples

## Not run: 
# Correlation matrix
data(iris)  # make sure its from 'datasets' package, not from 'locfit'
image(cor(as.matrix(iris[, names(iris) != "Species"])))

# Correlation matrix has diagonal from top left to bottom right
par(mar = c(1, 3, 1, 2))
image2(cor(as.matrix(iris[, names(iris) != "Species"])), col = "RdBu", axes = FALSE)

## End(Not run)
# Color histogram
nn <- 10
set.seed(nn)
AA <- matrix(sample(c(rnorm(nn^2, -1, 0.1), rexp(nn^2/2, 0.5))), ncol = nn)

image2(AA, col = "Spectral")
image2(y = 1:15 + 2, x = 1:10, AA, col = "Spectral", axes = TRUE)
image2(y = 1:15 + 2, x = 1:10, AA, col = "Spectral", density = TRUE, axes = TRUE)

image2(AA, col = "Spectral", density = TRUE, zlim = c(min(AA), 3))

Example output

LICORS documentation built on May 1, 2019, 10:13 p.m.