adegenet: pairDist – R documentation

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pairDist

Pairwise distance plots

Description

The function pairDistPlot extracts and plots pairwise distances between different groups (graphs use ggplot2). The function pairDistPlot does the same, without the graphs.

pairDistPlot is a generic function with methods for the following types of objects:
- dist
- matrix (only numeric data)
- genind objects (genetic markers, individuals)
- DNAbin objects (DNA sequences)

Usage

pairDist(x, ...)

pairDistPlot(x, ...)

## S3 method for class 'dist'
pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE,
             violin=TRUE, boxplot=TRUE, jitter=TRUE, ...)

## S3 method for class 'matrix'
pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE,
             violin=TRUE, boxplot=TRUE, jitter=TRUE, ...)

## S3 method for class 'genind'
pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE,
             violin=TRUE, boxplot=TRUE, jitter=TRUE, ...)

## S3 method for class 'DNAbin'
pairDistPlot(x, grp, within=FALSE, sep="-", data=TRUE,
             violin=TRUE, boxplot=TRUE, jitter=TRUE, ...)

Arguments

`x`	pairwise distances provided as a `dist` or a symmetric `matrix`, or `genind` or `DNAbin` object. For `genind` objects, pairwise squared Euclidean distances are computed from the allele data. For `DNAbin` objects, distances are computed uing `dist.dna`, and '...' is used to pass arguments to the function.
`grp`	a factor defining a grouping of individuals.
`within`	a logical indicating whether to keep within-group comparisons.
`sep`	a character used as separator between group names
`data`	a logical indicating whether data of the plot should be returned.
`violin`	a logical indicating whether a violinplot should be generated.
`boxplot`	a logical indicating whether a boxplot should be generated.
`jitter`	a logical indicating whether a jitter-plot should be generated.
`...`	further arguments to be used by other functions; used for `DNAbin` object to pass argumetns to `dist.dna`.

Value

A list with different components, depending on the values of the arguments. Plots are returned as ggplot2 objects.

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk.

Examples

## Not run: 

## use a subset of influenza data
data(H3N2)
set.seed(1)
dat <- H3N2[sample(1:nInd(H3N2), 100)]

## get pairwise distances
temp <- pairDistPlot(dat, other(dat)$epid)

## see raw data
head(temp$data)

## see plots
temp$boxplot
temp$violin
temp$jitter


## End(Not run)

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release