data.clust: Plot Hierarchical Cluster Of Samples Based on OTU Table or...
In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description Usage Arguments Value Author(s) Examples

This function plot hierarchical cluster Of ecology data set.

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)

`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.

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

Wen Chen

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)

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
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: "
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[1] "columns# with one level: "
[1] "column# that are not numeric or factor: 6"