initialize: Creating a hyperSpec Object Like other S4 objects, a...

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

Description

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

Usage

## S4 method for signature '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 plotmath). If label is not given, a list containing NULL for each of the columns ofdata and wavelength is used.

Author(s)

C.Beleites

See Also

new for more information on creating and initializing S4 objects.

plotmath on expressions for math annotations as for slot label.

hy.setOptions

Examples

new ("hyperSpec")

spc <- matrix (rnorm (12), ncol = 4)
new ("hyperSpec", spc = spc)
new ("hyperSpec", data = data.frame (x = letters[1:3]),
     spc = spc)

colnames (spc) <- 600:603
new ("hyperSpec", spc = spc)  # wavelength taken from colnames (spc)

# given wavelengths precede over colnames of spc
new ("hyperSpec", spc = spc, wavelength = 700:703)

# 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)

Example output

Loading required package: lattice
Loading required package: grid
Loading required package: ggplot2
Package hyperSpec, version 0.98-20161118

To get started, try
   vignette ("introduction", package = "hyperSpec")
   package?hyperSpec 
   vignette (package = "hyperSpec")

If you use this package please cite it appropriately.
   citation("hyperSpec")
will give you the correct reference.

The project homepage is http://hyperspec.r-forge.r-project.org


hyperSpec object
   0 spectra
   1 data columns
   0 data points / spectrum
wavelength:  [integer]
data:  (0 rows x 1 columns)
   1. spc:  [matrix0]
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:  [matrix4] -0.3458364 -0.6867826 ... -0.253361 
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:  [factor] a b c 
   2. spc:  [matrix4] -0.3458364 -0.6867826 ... -0.253361 
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:  [matrix4] -0.3458364 -0.6867826 ... -0.253361 
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:  [matrix4] -0.3458364 -0.6867826 ... -0.253361 
Warning message:
In plotc(h, spc ~ pos) : Intensity at first wavelengh only is used.

hyperSpec documentation built on May 2, 2019, 5:45 p.m.