pairDistPlot | R Documentation |
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)
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, ...)
x |
pairwise distances provided as a |
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
|
A list with different components, depending on the values of the
arguments. Plots are returned as ggplot2
objects.
Thibaut Jombart t.jombart@imperial.ac.uk.
gengraph
to identify connectivity based on distances.
## 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)
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