# seqalign: Computation details about a pairwise alignment In TraMineR: Trajectory Miner: a Toolbox for Exploring and Rendering Sequences

 seqalign 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)

`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.