Creating a hyperSpec Object

Like other S4 objects, a hyperSpec object can be created by new. The hyperSpec object is then initialized using the given parameters.

# S4 method for hyperSpec
initialize(.Object, spc = NULL, data = NULL, wavelength = NULL, labels = NULL)

Arguments

.Object	the new hyperSpec object.
spc	the spectra matrix. spc does not need to be a matrix, it is converted explicitly by I(as.matrix (spc)).
data	data.frame, possibly with the spectra in data$spc, and further variates in more columns. A matrix can be entered as one column of a data frame by: data.frame (spc = I (as.matrix (spc))). However, it will usually be more convenient if the spectra are given in spc
wavelength	The wavelengths corresponding to the columns of data. If no wavelengths are given, an appropriate vector is derived from the column names of data$spc. If this is not possible, 1:ncol(data$spc) is used instead.
labels	A list containing the labels for the columns of the data slot of the hyperSpec object and for the wavelength (in label$.wavelength). The labels should be given in a form ready for the text-drawing functions (see grDevices::plotmath()). If label is not given, a list containing NULL for each of the columns ofdata and wavelength is used.

Details

If option gc is TRUE, the initialization will have frequent calls to gc(), which can help to avoid swapping or running out of memory.

See also

methods::new() for more information on creating and initializing S4 objects.

grDevices::plotmath() on expressions for math annotations as for slot label.

hy.setOptions()

Author

C.Beleites

Examples

new("hyperSpec")
#> hyperSpec object
#>    0 spectra
#>    1 data columns
#>    0 data points / spectrum
#> wavelength:  [integer]
#> data:  (0 rows x 1 columns)
#>    1. spc:  [matrix, array0]

spc <- matrix(rnorm(12), ncol = 4)
new("hyperSpec", spc = spc)
#> hyperSpec object
#>    3 spectra
#>    1 data columns
#>    4 data points / spectrum
#> wavelength:  [integer] 1 2 3 4 
#> data:  (3 rows x 1 columns)
#>    1. spc:  [matrix, array4] -1.075224 -2.553725 ... -0.5495588 
new("hyperSpec",
  data = data.frame(x = letters[1:3]),
  spc = spc
)
#> hyperSpec object
#>    3 spectra
#>    2 data columns
#>    4 data points / spectrum
#> wavelength:  [integer] 1 2 3 4 
#> data:  (3 rows x 2 columns)
#>    1. x:  [character] a b c 
#>    2. spc:  [matrix, array4] -1.075224 -2.553725 ... -0.5495588 

colnames(spc) <- 600:603
new("hyperSpec", spc = spc) # wavelength taken from colnames (spc)
#> hyperSpec object
#>    3 spectra
#>    1 data columns
#>    4 data points / spectrum
#> wavelength:  [numeric] 600 601 602 603 
#> data:  (3 rows x 1 columns)
#>    1. spc:  [matrix, array4] -1.075224 -2.553725 ... -0.5495588 

# given wavelengths precede over colnames of spc
new("hyperSpec", spc = spc, wavelength = 700:703)
#> hyperSpec object
#>    3 spectra
#>    1 data columns
#>    4 data points / spectrum
#> wavelength:  [integer] 700 701 702 703 
#> data:  (3 rows x 1 columns)
#>    1. spc:  [matrix, array4] -1.075224 -2.553725 ... -0.5495588 

# specifying labels
h <- new("hyperSpec",
  spc = spc, data = data.frame(pos = 1:3),
  label = list(
    spc = "I / a.u.",
    .wavelength = expression(tilde(nu) / cm^-1),
    pos = expression("/"(x, mu * m))
  )
)

plot(h)
plotc(h, spc ~ pos)
#> Warning: Intensity at first wavelengh only is used.