RAM (version 1.2.1.3)

data.clust: Plot Hierarchical Cluster Of Samples Based on OTU Table or Taxonomic Abundance Matrix

Description

This function plot hierarchical cluster Of ecology data set.

Usage

data.clust(data, is.OTU=TRUE, meta, rank=NULL, top=NULL, mode="number", group=4, data.trans=NULL, dist=NULL, clust=NULL, type=NULL, main=NULL, file=NULL, ext=NULL, width=8, height=8)

Arguments

data

an ecology data set to be analyzed.

is.OTU

logical. If an OTU table was provided, is.OTU should be set as TRUE; otherwise, it should be set as FALSE.

meta

the metadata table associated with ecology data set.

rank

optional. If no rank was provided, the data will be used as it is, if rank is provided, if data is an OTU table, it will be converted to taxonomic abundance matrix at the given rank, no change will be made for a data that has already been a taxonomic abundance matrix. See also tax.abund and data.revamp

top

the top otuIDs or taxa to be considered for the clustering analysis. See also data.revamp

mode

either be "number" or "percent". See also data.revamp

group

an integer or a metadata variable. If an integar, will cut tree into corresponding groups and color them accordingly; if a metadata variable was provided, tree leaves (sampleIDs) will be colored by each level.

data.trans

optional. If was provided, numeric data will be transformed. See also decostand

dist

optional. If was provided, distance matrix will be calculated using the given method; otherwise use vegdist default Bray-Curtis method. See also vegdist and gowdis.

clust

optional. If was not provided, will use the default agglomeration method used by hclust, i.e. "complete". Otherwise, will used user defined method for clustering. See also hclust.

type

optional. Can be one of the following: "triangle", "rectangle", "phylogram", "cladogram", "fan", "unrooted", "radial".

main

The title of the plot.

file

optional. Filename that the plot to be saved to.

ext

optional. File type that the plot to be saved to.

width

an integer, width of the plot.

height

an integer, height of the plot.

Value

This function returns a tree plot of the hierarchical cluster of the samples based on ecological data.

Examples

data(ITS1, meta)
## Not run: 
# data.clust(data=ITS1, is.OTU=TRUE, data.trans="total", 
#            dist="bray", type="fan", meta=meta, group="Plots")
# ## End(Not run)