seqalign: Computation details about a pairwise alignment

Description

The function provides details about a pairwise alignment.

Usage

seqalign(seqdata, indices, indel=1, sm, with.missing = FALSE)
# S3 method for 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 seqalign
print(x, digits=3, ...)

Value

Object of class seqalign

Arguments

seqdata: a state sequence object defined with the seqdef function.
indices: a vector of length 2 giving the indexes of the two sequences
indel: indel cost (see seqdist)
sm: matrix of substitution costs or a method for computing the costs (see seqdist)
with.missing: logical: Should the missing state be considered as an element of the alphabet?
x: an object of class seqalign
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 par.
digits: number of digits for printed output
cex.plot: Deprecated. Use cex.axis instead.
...: additional arguments passed to other functions

Author

Alexis Gabadinho (plot.seqalign) and Matthias Studer (seqalign) (with Gilbert Ritschard for the help page)

Details

There are print and plot methods for seqalign objects.

Examples

Run this code

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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