# sampleDist: Compute the Distances Between Samples in a Spectra or... In ChemoSpecUtils: Functions Supporting Packages ChemoSpec and ChemoSpec2D

## 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

 `1` ```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

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29``` ```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" ) } ```

ChemoSpecUtils documentation built on Oct. 10, 2021, 5:06 p.m.