Computation details about a pairwise alignment
The function provides details about a pairwise alignment.
seqalign(seqdata, indices, indel=1, sm, with.missing = FALSE) ## S3 method for class 'seqalign' plot(x, cpal = NULL, missing.color = NULL, ylab = NULL, yaxis = TRUE, xaxis = TRUE, ytlab = NULL, ylas = 0, xtlab = NULL, cex.axis = 1, cex.plot, ...) ## S3 method for class 'seqalign' print(x, digits=3, ...)
seqdata |
a state sequence object defined with the |
indices |
a vector of length 2 giving the indexes of the two sequences |
indel |
indel cost (see |
sm |
matrix of substitution costs or a method for computing the costs (see |
with.missing |
logical: Should the missing state be considered as an element of the alphabet? |
x |
an object of class |
cpal |
color palette |
missing.color |
color for missing elements |
ylab |
y label |
yaxis |
yaxis |
xaxis |
xaxis |
ytlab |
ytlab |
ylas |
ylas |
xtlab |
xtlab |
cex.axis |
Axis annotation magnification. See |
digits |
number of digits for printed output |
cex.plot |
Deprecated. Use |
... |
additional arguments passed to other functions |
There are print and plot methods for seqalign objects.
Object of class seqalign
Alexis Gabadinho (plot.seqalign) and Matthias Studer (seqalign) (with Gilbert Ritschard for the help page)
data(biofam) biofam.seq <- seqdef(biofam, 10:25) costs <- seqsubm(biofam.seq, method="TRATE") sa <- seqalign(biofam.seq, 1:2, indel=1, sm=costs) print(sa) plot(sa) sa <- seqalign(biofam.seq, c(1,5), indel=0.5, sm=costs) print(sa) plot(sa)
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