sweep: Sweep Summary Statistic out of an hyperSpec Object 'sweep'...

In hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

Sweep Summary Statistic out of an hyperSpec Object sweep for hyperSpec objects.

Description

Calls sweep for the spectra matrix.

Usage

## S4 method for signature 'hyperSpec'
sweep(x, MARGIN, STATS, FUN = "-", check.margin = TRUE, ...)

Arguments

x	a hyperSpec object.
MARGIN	direction of the spectra matrix that STATS goees along.
STATS	the summary statistic to sweep out. Either a vector or a hyperSpec object. hyperSpec offers a non-standard convenience function: if STATS is a function, this function is applied first (with the same MARGIN) to compute the statistic. However, no further arguments to the apply function can be given. See the examples.
FUN	the function to do the sweeping, e.g. '-' or '/'.
check.margin	If TRUE (the default), warn if the length or dimensions of STATS do not match the specified dimensions of x. Set to FALSE for a small speed gain when you know that dimensions match.
...	further arguments for FUN

Details

sweep is useful for some spectra preprocessing, like offset correction, substraction of background spectra, and normalization of the spectra.

Value

A hyperSpec object.

Author(s)

C. Beleites

See Also

sweep

Examples

## Substract the background / slide / blank spectrum
# the example data does not have spectra of the empty slide,
# so instead the overall composition of the sample is substracted
background <- apply (chondro, 2, quantile, probs = 0.05)
corrected <- sweep (chondro, 2, background, "-")
plot (corrected, "spcprctl5")

## Offset correction
offsets <- apply (chondro, 1, min)
corrected <- sweep (chondro, 1, offsets, "-")
plot (corrected, "spcprctl5")

## Min-max normalization (on max amide I)
# the minimum is set to zero by the offset correction.
factor <- apply (corrected, 1, max)
mm.corrected <- sweep (corrected, 1, factor, "/")
plot (mm.corrected, "spcprctl5")

## convenience: give function to compute STATS:
mm.corrected2 <- sweep (corrected, 1, max, "/")
plot (mm.corrected2)

## checking
stopifnot (all (mm.corrected2 == mm.corrected))

hyperSpec documentation built on May 29, 2024, 7:28 a.m.