R: Visualises clusters of markers vs. species

lociplots {prabclus} | R Documentation

## 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 chrish@stats.ucl.ac.uk http://www.homepages.ucl.ac.uk/~ucakche

### See Also

`prabclust`

### 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)

[Package prabclus version 2.2-6 Index]