adegenet (version 2.0.0)

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

Arguments

x

pairwise distances provided as a dist or a symmetric matrix, or genind or DNAbin object. For genind objects, pairwise squared

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.

encoding

UTF-8

See Also

gengraph to identify connectivity based on distances.

Examples

## 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