haploNet {pegas} | R Documentation |
haploNet
computes a haplotype network. There is a plot method.
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, ...)
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 . |
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.
Emmanuel Paradis
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.
## 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)