haploNet {pegas}R Documentation

Haplotype Networks

Description

haploNet computes a haplotype network. There is a plot method.

Usage

haploNet(h)
## S3 method for class 'haploNet':
plot(x, size = 1, col = "black", bg = "white",
     col.link = "black", lwd = 1, lty = 1, pie = NULL,
     labels = TRUE, font = 2, cex = 1, scale.ratio = 1,
     legend = FALSE, fast = FALSE, ...)

Arguments

h an object of class "haplotype".
x an object of class "haploNet".
size a numeric vector giving the diameter of the circles representing the haplotypes: this is in the same unit than the links and eventually recycled.
col a character vector specifying the colours of the circles; eventually recycled.
bg a character vector specifying the colours of the background of the circles; eventually recycled.
col.link a character vector specifying the colours of the links; eventually recycled.
lwd a numeric vector giving the width of the links; eventually recycled.
lty idem for the line types.
pie a matrix used to draw pie charts for each haplotype; it must have as many rows as there is haplotypes.
labels a logical specifying whether to identify the haplotypes with their labels (the default).
font the font used for these labels (bold by default); must an integer between 1 and 4.
cex a numerical specifying the character expansion of the labels.
scale.ratio the ratio of the scale of the links representing the number of steps on the scale of the circles representing the haplotypes. It may be needed to give a value greater than one to avoid overlapping circles.
legend a logical specifying whether to draw the legend, or a vector of length two giving the coordinates where to draw the legend; FALSE by default. If TRUE, the user is asked to click where to draw the legend.
fast a logical specifying whether to optimize the spacing of the circles; FALSE by default.
... further arguments passed to plot.

Value

haploNet returns an object of class "haploNet" which is a matrix where each row represents a link in the network, the first and second columns give the numbers of the linked haplotypes, the third column, named "step", gives the number of steps in this link, and the fourth column, named "Prob", gives the probability of a parsimonious link as given by Templeton et al. (1992). There are two additional attributes: "freq", the absolute frequencies of each haplotype, and "labels", their labels.

Author(s)

Emmanuel Paradis

References

Templeton, A. R., Crandall, K. A. and Sing, C. F. (1992) A cladistic analysis of phenotypic association with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619–635.

See Also

haplotype

Examples

## generate some artificial data from 'woodmouse':
data(woodmouse)
x <- woodmouse[sample(15, size = 110, replace = TRUE), ]
h <- haplotype(x)
(net <- haploNet(h))
plot(net)
## symbol sizes equal to haplotype sizes:
plot(net, size = attr(net, "freq"), fast = TRUE)
plot(net, size = attr(net, "freq"))
plot(net, size=attr(net, "freq"), scale.ratio = 2, cex = 0.8)

[Package pegas version 0.3 Index]