seqalign: Computation details about a pairwise alignment

View source: R/seqalign.R

seqalignR Documentation

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 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, ...)

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

Details

There are print and plot methods for seqalign objects.

Value

Object of class seqalign

Author(s)

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

See Also

seqdist

Examples

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)

TraMineR documentation built on Dec. 1, 2022, 5:08 p.m.