META.clust: Plot Hierarchical Cluster Of Metadata

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description

This function plot hierarchical cluster Of metadata.

Usage

META.clust(meta, group=4, data.trans=NULL, dist=NULL, 
           clust=NULL, type=NULL, main="", file=NULL, 
           ext=NULL, width=8, height=8)

Arguments

meta	the metadata table to be clustered.
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 provided, numeric data will be transformed. See also decostand
dist	optional. If provided, distance matrix will be calculated using the give method for numeric variables; otherwise use vegdist default Bray-Curtis method. If metadata include qualitative variables, distance matrix will be calculated by gowdis.
clust	optional. If 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 return a plot of the hierarchical cluster analysis on a set of metadata.

Author(s)

Wen Chen

See Also

vegdist and gowdis.

Examples

data(meta)
META.clust(meta=meta, type="fan")
META.clust(meta=meta, type="fan", group="City")
META.clust(meta=meta, type="rectangle", group="Harvestmethod")
META.clust(meta=meta, type="triangle", group="City", 
          clust="average")

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
[1] "A total of  1  columns are removed:  Harvestdate"
[1] "columns in exclude list: "
[1] "column# with missing data: "
[1] "columns# with one level: "
[1] "column# that are not numeric or factor: 6"
[1] "A total of  1  columns are removed:  Harvestdate"
[1] "columns in exclude list: "
[1] "column# with missing data: "
[1] "columns# with one level: "
[1] "column# that are not numeric or factor: 6"
[1] "A total of  1  columns are removed:  Harvestdate"
[1] "columns in exclude list: "
[1] "column# with missing data: "
[1] "columns# with one level: "
[1] "column# that are not numeric or factor: 6"
[1] "A total of  1  columns are removed:  Harvestdate"
[1] "columns in exclude list: "
[1] "column# with missing data: "
[1] "columns# with one level: "
[1] "column# that are not numeric or factor: 6"

RAM documentation built on May 2, 2019, 3:04 p.m.