prabclus: lociplots – R documentation

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lociplots

Visualises clusters of markers vs. species

Description

Given a clustering of individuals from prabclust (as generated in species delimitation) and a clustering of markers (for example dominant markers of genetic loci), lociplots visualises the presence of markers against the clustering of individuals and computes some statistics.

Usage

lociplots(indclust,locclust,locprab,lcluster,
                      symbols=NULL,brightest.grey=0.8,darkest.grey=0,
                      mdsdim=1:2)

Arguments

`indclust`	`prabclust`-object. Clustering of individuals.
`locclust`	vector of integers. Clustering of markers/loci.
`locprab`	`prab`-object in which the markers are what the help page of `prabinit` refers to as "species" (i.e., reverse of what is used for species delimitation clustering; for data sets with codominant markers, such an object can be constructed by use of `allele2zeroone` before `prabinit`.)
`lcluster`	integer. Number of cluster in `locclust` for which plot and statistics are produced.
`symbols`	vector of plot symbols. If `NULL`, `indclust$symbols` is used.
`brightest.grey`	numeric between 0 and 1. Brightest grey value used in plot for individuals with smallest marker percentage, see details.
`darkest.grey`	numeric between 0 and 1. Darkest grey value used in plot for individuals with highest marker percentage, see details.
`mdsdim`	vector of two integers. The two MDS variables taken from `indclust` used for visualisation.

Details

Plot and statistics are based on the individual marker percentage, which is the percentage of markers present in an individual of the markers belonging to cluster no. lcluster. In the plot, the grey value visualises the marker percentage.

Value

list with components

`locfreq`	vector of individual marker percentages.
`locfreqmin`	vector of minimum individual marker precentages for each cluster in `indclust`-clustering (the first value refers to the "noise component", if present).
`locfreqmax`	vector of maximum individual marker precentages for each cluster in `indclust`-clustering (the first value refers to the "noise component", if present).
`locfreqmean`	vector of average individual marker precentages for each cluster in `indclust`-clustering (the first value refers to the "noise component", if present).

Author(s)

Christian Hennig christian.hennig@unibo.it https://www.unibo.it/sitoweb/christian.hennig/en

Examples

options(digits=4)
  data(veronica)
  vei <- prabinit(prabmatrix=veronica[1:50,],distance="jaccard")
  ppv <- prabclust(vei)
  veloci <- prabinit(prabmatrix=veronica[1:50,],rows.are.species=FALSE)
  velociclust <- prabclust(veloci,nnk=0)
  lociplots(ppv,velociclust$clustering,veloci,lcluster=3)

prabclus

Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data

v2.3-2

GPL

Authors

Christian Hennig <christian.hennig@unibo.it>, Bernhard Hausdorf <Hausdorf@zoologie.uni-hamburg.de>

Initial release

2020-01-06