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 al
top
the top otuIDs or taxa to be considered for the clustering analysis.
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.