sweep: Sweep Summary Statistic out of an hyperSpec Object 'sweep'...
In hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

Description Usage Arguments Details Value Author(s) See Also Examples

Calls sweep for the spectra matrix.

1 2	## S4 method for signature 'hyperSpec' sweep(x, MARGIN, STATS, FUN = "-", check.margin = TRUE, ...)

`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`

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

A hyperSpec object.

C. Beleites

sweep

## 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))