plotmap: Plot a Map and Identify Spectra

Description

An image or map of a summary value of each spectrum is plotted. The spectra may be identified by mouse click.

Usage

plotmap (object, x = "x", y = "y", func = mean, cond = NULL, 
         z = NULL, do.print = FALSE, print.args = NULL, trellis.args = NULL,
         ...)
map.identify (object, x = "x", y = "y", ...)

Arguments

object

the hyperSpec object

x, y

names of the columns in slot @data to be used as x and y coordinates

func

function to apply to compute the summary statistic that is displayed if z is not given.

cond

conditioning factor (for | cond in the levelplot formula). May also be the name of the extra data column to be used for conditioning.

summary value to be displayed. If z is a factor, and the default color scheme (returned by matlab.palette) is used, one color per level of z is used, othe

do.print

if TRUE, the lattice object is printed with the further arguments given in print.args before returning it.

print.args

list with further arguments for printing the lattice object.

trellis.args

list with further arguments passed to levelplot.

...

further arguments passed to func by plotmap.

map.identify passes all further arguments to plotmap.

Value

a lattice object

Details

plotmap calculates a grid (via index.grid) on which the summary value is displayed with levelplot.

Arguments to levelplot can be given in trellis.args.

map.identify calls plotmap and waits for (left) mouse clicks on points. The row indices of the

Examples

Run this code

background <- apply (chondro, 2, quantile, probs = 0.05)
corrected <- sweep (chondro, 2, background, "-")

plotmap (corrected, func = max)

plotmap (corrected, func = max,
         trellis.args = list (col.regions = gray ((100 : 0)/100))
        )


dist <- pearson.dist (chondro[[]])
dend <- hclust (dist, method = "ward")
z <- cutree (dend, h = 0.15)

plotmap (chondro, z = z)

plotmap (chondro, z = as.factor (z))