R: Computation details about a pairwise alignment

seqalign {TraMineR} | R 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)

[Package TraMineR version 2.2-3 Index]