getPrincipalCoordinates: Get principal coordinates for the samples in an ftmsData...

In EMSL-Computing/fticRanalysis: Analysis and visualization tools for FT-MS data

Get principal coordinates for the samples in an ftmsData object

Description

Calculate the principal coordinates of the samples in an ftmsData object. Uses vegdist to calculate pairwise distances between samples, and pcoa to calculate the principal coordinates.

Usage

getPrincipalCoordinates(ftmsObj, dist_metric = "bray", n_dims = 5)

Arguments

ftmsObj	object of type ftmsData
dist_metric	distance metric for computing pairwise distances between all samples. See vegdist for options. Default is "bray".
n_dims	number of dimensions to return, default is 5. Must be less than the number of samples in ftmsObj

Value

data.frame of coordinates where each sample is a row

See Also

vegdist, pcoa

Examples

coords <- getPrincipalCoordinates(exampleProcessedPeakData, dist_metric="jaccard", n_dims=7)

EMSL-Computing/fticRanalysis documentation built on March 23, 2024, 8:36 p.m.