mutations | R Documentation |
mutations
draws annotations about mutations related to the link
of a haplotype network.
mutations(haploNet, link, x, y, data = NULL, style = "table", POS, SEQLEN, ...)
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 |
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"
.
none
Emmanuel Paradis
plot.haploNet
, haplotype.loci
## 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")
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