OPTICSplot: Visualisation of density-based clustering of spectral...

In CluMSID: Clustering of MS2 Spectra for Metabolite Identification

Description

OPTICSplot() performs density-based clustering of spectral similarity data using the OPTICS algorithm like OPTICStbl and creates a reachability distance plot.

Usage

OPTICSplot(distmat, eps = 10000, minPts = 3, eps_cl = 0.5, ...)

Arguments

distmat	A distance matrix as generated by distanceMatrix.
eps	OPTICS parameters, see optics.
minPts	OPTICS parameters, see optics.
eps_cl	The reachability distance used for cluster determination, see extractDBSCAN.
...	Additional graphical parameters to be passed to plot()

Details

The function internally uses optics and extractDBSCAN from the dbscan package.

Value

A reachability distance plot as visualisation of OPTICS clustering, see codeextractDBSCAN.

See Also

OPTICStbl

Examples

load(file = system.file("extdata",
    "distmat.RData",
    package = "CluMSIDdata"))

OPTICSplot(distmat[1:50,1:50], eps_cl = 0.7)

CluMSID documentation built on Nov. 8, 2020, 7:46 p.m.