Plot a map and identify/select spectra in the map

lattice::levelplot() functions for hyperSpec objects. An image or map of a summary value of each spectrum is plotted. Spectra may be identified by mouse click.

plot_map(object, model = spc ~ x * y, func = mean, func.args = list(), ...)

# S4 method for formula,hyperSpec
levelplot(
  x,
  data,
  transform.factor = TRUE,
  ...,
  contour = FALSE,
  useRaster = !contour
)

# S4 method for hyperSpec,missing
levelplot(x, data, ...)

map.identify(
  object,
  model = spc ~ x * y,
  voronoi = FALSE,
  ...,
  tol = 0.02,
  warn = TRUE
)

plot_voronoi(
  object,
  model = spc ~ x * y,
  use.tripack = "DEPRECATED",
  mix = "DEPRECATED",
  ...
)

Arguments

object, data

the hyperSpec object

model, x

formula specifying the columns of object that are to be displayed by lattice::levelplot()

func, func.args

Before plotting, plot_map applies function func with the arguments given in the list func.args to each of the spectra. Thus a single summary value is displayed for each of the spectra.

This can be suppressed manually by setting func to NULL. It is automatically suppressed if .wavelength appears in the formula.

...

further arguments are passed down the call chain, and finally to lattice::levelplot()

transform.factor

If the color-coded variable is a factor, should trellis.factor.key() be used to compute the color coding and legend?

contour, useRaster

see lattice::levelplot()

voronoi

Should the plot for identifying spectra by mouse click be produced by plot_map (default) or plot_voronoi?

tol

tolerance for map.identify as fraction of the viewport (i.e. in "npc" units)

warn

should a warning be issued if no point is within the specified tolerance? See also details.

use.tripack

(DEPRECATED) See latticeExtra::panel.voronoi for details.

mix

(DEPRECATED) This argument is deprecated due to deprecation of argument use.tripack.

Value

map.identify returns a vector of row indices into object of the clicked points.

The other functions return a lattice object.

Details

The model can contain the special column name .wavelength to specify the wavelength axis.

plot_map, map.identify, and the levelplot methods internally use the same gateway function to lattice::levelplot(). Thus transform.factor can be used with all of them and the panel function defaults to lattice::panel.levelplot.raster() for all three. Two special column names, .rownames and .wavelength may be used.

levelplot plots the spectra matrix.

plot_voronoi calls plot_map with different default settings, namely the panel function defaults to latticeExtra::panel.voronoi(). latticeExtra::panel.voronoi() depends on either of the packages interp or deldir being installed. For further information, please consult the help page of latticeExtra::panel.voronoi().

map.identify() calls plot_map() and plot_voronoi(), respectively and waits for (left) mouse clicks on points. Other mouse clicks end the input.

Unlike lattice::panel.identify(), the indices returned by map.identify are in the same order as the points were clicked. Also, multiple clicks on the same point are returned as multiple entries with the same index.

map.identify uses option debuglevel similar to identify_spc(): debuglevel == 1 will plot the tolerance window if no data point was inside (and additionally labels the point) while debuglevel == 2 will always plot the tolerance window.

The map.sel.* functions offer further interactive selection, see map.sel.poly().

Author

C. Beleites

Examples

if (FALSE) {
vignette(plotting)
vignette(hyperSpec)
}

levelplot(spc ~ y * x, faux_cell[, , 1003]) # properly rotated
#> Warning: device support for raster images unknown, ignoring 'raster=TRUE'

plot_map(faux_cell[, , 1003])
#> Warning: device support for raster images unknown, ignoring 'raster=TRUE'


# plot spectra matrix
levelplot(spc ~ .wavelength * t, laser, contour = TRUE, col = "#00000080")

# see also plot_matrix

plot_map(faux_cell, region ~ x * y)
#> Warning: device support for raster images unknown, ignoring 'raster=TRUE'


# Voronoi plots
smpl <- sample(faux_cell, 300)
plot_map(smpl, region ~ x * y)
#> Warning: device support for raster images unknown, ignoring 'raster=TRUE'


plot_voronoi(smpl, region ~ x * y)
#> Warning: device support for raster images unknown, ignoring 'raster=TRUE'