ngsLCA_NMDS: Taxa Profiles NMDS
In wyc661217/ngsLCA: Process and Visualize Lca Files and Taxonomic Profiles

View source: R/ngsLCA_NMDS.R

ngsLCA_NMDS

R Documentation

Taxa Profiles NMDS

Description

Perform Non-metric Multidimensional Scaling (NMDS) on taxa profiles. Results will be in "path/run/NMDS/". See vegan::metaMDS for details.

Usage

ngsLCA_NMDS(path, run = "run01", dimension = 3, trymax = 100)

Arguments

`path`	working directory, same to `ngsLCA_profile`.
`run`	name of the run, default is "run01".
`dimension`	dimension of the NMDS; default is 3.
`trymax`	maximum number of random starts in search of convergent solutions for NMDS; default is 100.

Value

R data files for NMDS results, figures for NMDS stressplots, cluster figures for the first 2 NMDS components.

Examples

## Not run: ngsLCA_NMDS(path=system.file("extdata","lca_files",package="ngsLCA"),
            run="run01",
            dimension=3,
            trymax=1000)
## End(Not run)


## This will perform NMDS on the complete taxa
## profile as well as taxa groups and ranks
## (if available) of "run01". Results will be in
## "path/run01/NMDS/".

wyc661217/ngsLCA documentation built on June 2, 2025, 12:02 a.m.