Plotting hyperSpec Objects.

The plot method for hyperSpec objects is a switchyard to plotspc(), plotmap(), and plotc().

# S4 method for hyperSpec,missing
plot(x, y, ...)

# S4 method for hyperSpec,character
plot(x, y, ...)

Arguments

x	the hyperSpec object
y	selects what plot should be produced
...	arguments passed to the respective plot function

Details

It also supplies some convenient abbrevations for much used plots.

If y is missing, plot behaves like plot(x, y = "spc").

Supported values for y are:

"spc"

calls plotspc() to produce a spectra plot.

"spcmeansd"

plots mean spectrum +/- one standard deviation

"spcprctile"

plots 16th, 50th, and 84th percentile spectre. If the distributions of the intensities at all wavelengths were normal, this would correspond to "spcmeansd". However, this is frequently not the case. Then "spcprctile" gives a better impression of the spectral data set.

"spcprctl5"

like "spcprctile", but additionally the 5th and 95th percentile spectra are plotted.

"map"

calls plotmap() to produce a map plot.

"voronoi"

calls plotvoronoi() to produce a Voronoi plot (tesselated plot, like "map" for hyperSpec objects with uneven/non-rectangular grid).

"mat"

calls plotmat() to produce a plot of the spectra matrix (not to be confused with graphics::matplot()).

"c"

calls plotc() to produce a calibration (or time series, depth-profile, or the like).

"ts"

plots a time series: abbrevation for plotc(x, use.c = "t").

"depth"

plots a depth profile: abbrevation for plotc(x, use.c = "z").

See also

plotspc() for spectra plots (intensity over wavelength),

plotmap() for plotting maps, i.e. color coded summary value on two (usually spatial) dimensions.

plotc()

graphics::plot()

Author

C. Beleites

Examples

plot(flu)

plot(flu, "c")
#> Warning: Intensity at first wavelengh only is used.

plot(laser, "ts")
#> Warning: Intensity at first wavelengh only is used.

spc <- apply(faux_cell, 2, quantile, probs = 0.05)
spc <- sweep(faux_cell, 2, spc, "-")
plot(spc, "spcprctl5")
plot(spc, "spcprctile")
plot(spc, "spcmeansd")

### use plotspc as default plot function