plotParamBCC: Get indices for barcode-cluster plotting

In eberlejonas/TaxCI: Calculate the Consistency Index and the Retention Index for taxonomic data

Description

Summarizes the output from BCCluster and outputs indices for plotting on the tree.

Usage

plotParamBCC(tree, x, BCCluster.result, plotParamTCI.result, cluster.nodes = TRUE)

Arguments

tree	The tree that will be plotted later.
x	A table with taxonomic information (must contain a column with species names which is specified with sp.col). Must be the same one that was used in the previous BCCluster-analysis.
BCCluster.result	The list that resulted from a BCCluster-analysis.
plotParamTCI.result	The list that resulted from a plotParamTCI-analysis.
cluster.nodes	Logical. Should the mrca-node number of each cluster containing more than 1 specimen be saved for later visualization with TaxCIplot? Will take quiet a while for large trees.

Details

This function is usefull for further processing the output of an BCCluster-analysis.

Value

A list containing the following elements:

sp.in.het.clust	A vector of all species that appear in heterogeneous clusters.
spn.in.het.clust	A vector of all specimens that appear in heterogeneous clusters.
species.in.n.clusters	Named integer vector with numbers of clusters in which a species occur.
spn.in.het.clust2	Character vector of all specimens that appear in heterogeneous clusters AND whichs species appear in another cluster.
rel.abundance	List of relative abundances of species in heterogeneous clusters.
rel.abundance.spn	Named vector of relative abundances of all specimens in heterogeneous clusters.
spn.marked.by.rel.abund	Character vector of specimens in heterogeneous clusters which don't have the lowest relative abundance.
splitted.species.homogen	Species that appear in more than one homogeneous cluster.
spn.in.split.hom.clust	Specimens in splitted.species.homogen.
relevant.species	A vector of all specimens that might be problematic.
i	index for tree$tip.label of specimens that are in heterogeneous clusters
j	index for tree$tip.label of specimens that are in heterogeneous clusters and occur in more than one cluster
k	index for tree$tip.label of specimens that are marked because they didn't have the highest relative abundance in a heterogeneous cluster.
l	index for tree$tip.label of specimens which belong to species that appear in more than one homogeneous cluster
m	index for tree$tip.label of all relevant specimen
tips	a vector 1:number_of_tips_in_tree. Usefull for plottig something on all tips except the indexed (tips[-i])
mrca.clusters	Only available if cluster.nodes = TRUE. Contains node numbers of tree that are most recent common ancestors of a cluster.

Author(s)

Jonas Eberle

See Also

See TaxCI for example.

Related: BCCluster

eberlejonas/TaxCI documentation built on July 20, 2021, 9:46 a.m.