haploNet: Haplotype Networks

Description Usage Arguments Details Value Note Author(s) References See Also Examples

View source: R/haplotype.R

Description

haploNet computes a haplotype network. There is a plot method and two conversion functions towards other packages.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
haploNet(h, d = NULL, getProb = TRUE)
## S3 method for class 'haploNet'
print(x, ...)
## S3 method for class 'haploNet'
plot(x, size = 1, col, bg, col.link, lwd, lty,
     shape = "circles", pie = NULL, labels, font, cex, scale.ratio,
     asp = 1, legend = FALSE, fast = FALSE, show.mutation,
     threshold = c(1, 2), xy = NULL, ...)
## S3 method for class 'haploNet'
as.network(x, directed = FALSE, altlinks = TRUE, ...)
## S3 method for class 'haploNet'
as.igraph(x, directed = FALSE, use.labels = TRUE,
        altlinks = TRUE, ...)
## S3 method for class 'haploNet'
as.phylo(x, quiet, ...)
## S3 method for class 'haploNet'
as.evonet(x, ...)

Arguments

h

an object of class "haplotype".

d

an object giving the distances among haplotypes (see details).

getProb

a logical specifying whether to calculate Templeton's probabilities (see details).

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 either the colours of the background of the circles (if pie = NULL), or the colours of the slices of the pies; 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.

shape

the symbol shape used for the haplotypes (eventually recycled): "circles", "squares", "diamonds" (can be abbreviated).

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; 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.

show.mutation

an integer value: if 0, nothing is drawn on the links; if 1, the mutations are shown with small segments on the links; if 2, they are shown with small dots; if 3, the number of mutations are printed on the links.

threshold

a numeric vector with two values (or 0) giving the lower and upper numbers of mutations for alternative links to be displayed. If threshold = 0, alternative links are not drawn at all.

directed

a logical specifying whether the network is directed (FALSE by default).

use.labels

a logical specifying whether to use the original labels in the returned network.

altlinks

whether to output the alternative links when converting to another class; TRUE by default.

quiet

whether to give a warning when reticulations are dropped when converting a network into a tree.

xy

the coordinates of the nodes (see replot).

...

further arguments passed to plot.

Details

By default, the haplotype network is built using an infinite site model (i.e., uncorrected or Hamming distance) of DNA sequences and pairwise deletion of missing data (see dist.dna). Users may specify their own distance with the argument d. There is no check of labels, so the user must make sure that the distances are ordered in the same way than the haplotypes.

The probabilities calculated with Templeton et al.'s (1992) method may give non-finite values with very divergent sequences, resulting in an error from haploNet. If this happens, it may be better to use getProb = FALSE.

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 three additional attributes: "freq", the absolute frequencies of each haplotype, "labels", their labels, and "alter.links", the alternative links of the network.

as.network and as.igraph return objects of the appropriate class.

Note

If two haplotypes are very different, haploNet will likely fail (error during integration due to non-finite values).

Author(s)

Emmanuel Paradis, Klaus Schliep

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, haploFreq, replot, diffHaplo, mst, mjn

Examples

 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)

Example output

Loading required package: ape
Loading required package: adegenet
Loading required package: ade4
Registered S3 method overwritten by 'spdep':
  method   from
  plot.mst ape 

   /// adegenet 2.1.3 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()


Registered S3 method overwritten by 'pegas':
  method      from
  print.amova ade4

Attaching package:pegasThe following object is masked frompackage:ade4:

    amova

The following object is masked frompackage:ape:

    mst

Haplotype network with:
  15 haplotypes
  68 links
  link lengths between 2 and 14 steps

Use print.default() to display all elements.

pegas documentation built on May 17, 2021, 9:08 a.m.