sampleDist {ChemoSpecUtils}

Compute the Distances Between Samples in a Spectra or Spectra2D Object

Description

Compute the distances between samples in a Spectra or Spectra2D object. This is a means to quantify the similarity between samples. A heat map style plot is an option.

Usage

sampleDist(spectra, method = "pearson", plot = TRUE, ...)

Arguments

spectra

An object of S3 class ChemoSpec::Spectra() or ChemoSpec2D::Spectra2D().

method

Character. A string giving the distance method. See rowDist for options.

plot

Logical. Shall a level plot (heat map) be made?

...

Parameters to be passed to the plotting routines. Applies to base graphics only.

Value

A numeric matrix giving the distances between the samples.

Author(s)

Bryan A. Hanson (DePauw University).

See Also

For Spectra objects, see plotSpectraDist which compares all spectra to a single reference spectrum.

Examples

# You need to install package "lattice" for this example
if (requireNamespace("lattice", quietly = TRUE)) {
  if (checkForPackageWithVersion("ChemoSpec", 6.0)) {
    library("ChemoSpec")
    library("lattice")
    data(SrE.IR)

    SrE.dmatrix <- sampleDist(SrE.IR, # cosine distance bounded on [0...2]
      method = "cosine",
      main = "SrE.IR Cosine Distance Between Samples"
    )
    SrE.dmatrix <- sampleDist(SrE.IR, # abspearson distance bounded on [0...1]
      method = "abspearson",
      main = "SrE.IR Absolute Pearson Distance Between Samples"
    )
    SrE.dmatrix <- sampleDist(SrE.IR, # euclidean distance unbounded
      method = "euclidean",
      main = "SrE.IR Euclidean Distance Between Samples"
    )
  }

  if (checkForPackageWithVersion("ChemoSpec2D", 0.5)) {
    library("ChemoSpec2D")
    library("lattice")
    data(MUD1)

    MUD1.dmatrix <- sampleDist(MUD1,
      method = "cosine",
      main = "MUD1 Cosine Distance Between Samples"
    )
  }
}