| mutations {pegas} | R Documentation |
Plot Mutations on Networks
Description
mutations draws annotations about mutations related to the link
of a haplotype network.
Usage
mutations(haploNet, link, x, y, data = NULL, style = "table", POS, SEQLEN, ...)
Arguments
haploNet |
an object of class |
link |
the link number; can be left missing in which case the list of links in the network is printed and the function exits. |
x, y |
the coordinates where to draw the annotations; can be left missing: the user is then asked to click where to draw them and the chosen coordinates are printed. |
data |
the sequence data; can be left missing if the data are
attached to the network (for a MJN network output by
|
style |
the type annotations. There two possible choices:
|
POS, SEQLEN |
a vector of genomic positions and the sequence
length in case |
... |
options |
Details
The easiest way to use this function is with an output from
mjn since the data are attached to the network. In other
cases, the sequence data must given to the argument data or
attached to the network as an attribute named "data".
Value
none
Author(s)
Emmanuel Paradis
See Also
Examples
## simple example
x <- as.DNAbin(matrix(c("a", "g"), 2, 1))
rownames(x) <- paste("Ind", 1:2, sep = "_")
nt <- mst(dist.dna(x, "N"))
plot(nt)
mutations(nt, link = 1, x = 2, y = 2, data = x)
example(mjn)
plot(ntz, xlim = c(-5, 20))
mutations(ntz, 6, 10, 0, style = "s")
mutations(ntz, 8, 10, -2, style = "s")