R: Plotting Edit Transcripts and Sequence Alignments

plot.sdists.graph {cba} | R Documentation

## Plotting Edit Transcripts and Sequence Alignments

### Description

Function for visualizing the optimal transformation (alignment) graph for two symbol sequences.

### Usage

    ## S3 method for class 'sdists.graph'
    plot(x, circle.col = 1, graph.col = 2,
         circle.scale = c("mean", "max", "last", "text"), main = "", ...)

### Arguments

`x` | an object of class `sdists.graph.`
`circle.col` | color to be used for circles.
`graph.col` | color to be used for the graph.
`circle.scale` | scaling to be used for circles.
`main` | plot title.
`...` | further unused arguments.

### Details

This function plots the dynamic programming table, the (back)pointers and the combined graph of optimal edit transcripts (alignments) computed with `sdist.trace`. The fist sequence is represented by the y-axis and the second by the x-axis.

The circumference of a circle is proportional to the minimum cost (maximum weight) of edit (alignment) operations leading to a table cell. `circle.scale` specifies the type of normalization performed where `last` means the last table entry (containing the optimum value), and `text` draws the values instead of circles.

The (back)pointers, defining possible (traceback) paths, are plotted as `dotted` edges. Note that a traceback starts in the last cell of the table and ends at the origin.

For the edges of the graph that is the union of all optimal paths, two line types are used: `solid` for insert, delete, and replace operations, and `dashed` for a match. The line width indicates the number of times an edge is on a path, but note that the interpretation is device-specific (compare `par`).

### Note

Some issues with grid were fixed in R.2.4.x (Fixme ?).

### Author(s)

Christian Buchta

### References

D. Gusfield (1997). Algorithms on Strings, Trees, and Sequences. Cambridge University Press, Chapter 11.

Inspired by: http://home.uchicago.edu/~aabbott/.

### See Also

`sdists.trace`, `plot`

### Examples

    ## continue example in sdists.trace
    x1 <- "vintner"
    y1 <- "writers"
    b11 <- sdists.trace(x1, y1, weight=c(1,1,0,1), graph = TRUE)
    b11
    plot(b11)
    plot(b11, circle.scale = "text")
    ## partial
    b12 <- sdists.trace(x1, y1, weight=c(1,1,0,1), graph = TRUE, partial = TRUE)
    b12
    plot(b12)

[Package cba version 0.2-21 Index]