sampleDist {ChemoSpecUtils} R Documentation

## 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 `Spectra` or `Spectra2D`. `method` Character. A string giving the distance method. See `rowDist` for options. `plot` Logical. Shall a level plot (heat map) be made? `...` Arguments to be passed to the plotting function.

### 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

```
if (checkForPackageWithVersion("ChemoSpec", "5.1")) {
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", "0.3")) {
library("ChemoSpec2D")
library("lattice")
data(MUD1)

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

[Package ChemoSpecUtils version 0.4.96 Index]