Description Usage Arguments Details Value Author(s) References See Also Examples
haploNet
computes a haplotype network. There is a plot method
and two conversion functions towards other packages.
1 2 3 4 5 6 7 8 9 10 | haploNet(h, d = NULL)
## 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,
asp = 1, legend = FALSE, fast = FALSE, ...)
## S3 method for class 'haploNet'
as.network(x, directed = FALSE, ...)
## S3 method for class 'haploNet'
as.igraph(x, directed = FALSE, use.labels = TRUE, ...)
|
h |
an object of class |
d |
an object giving the distances among haplotypes (see details). |
x |
an object of class |
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; its number of rows must be equal to the number of 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 be 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. |
asp |
the aspect ratio of the plot. Do not change the default unless you want to distort your network. |
legend |
a logical specifying whether to draw the legend, or a
vector of length two giving the coordinates where to draw the
legend; |
fast |
a logical specifying whether to optimize the spacing of
the circles; |
directed |
a logical specifying whether the network is directed
( |
use.labels |
a logical specifying whether to use the original labels in the returned network. |
... |
further arguments passed to |
By default, the haplotype network is built using an infinite site
model (i.e., uncorrected or Hamming distance). Users may specify their
own distance with the argument d
. Currently, there is no check
of labels, so the user must make sure that the distances are ordered
in the same way than the haplotypes.
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.
as.network
and as.igraph
return objects of the
appropriate class.
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.
1 2 3 4 5 6 7 8 9 10 | ## 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)
|
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