Function for visualizing the optimal transformation (alignment) graph for two symbol sequences.
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an object of class
color to be used for circles.
color to be used for the graph.
scaling to be used for circles.
further unused arguments.
This function plots the dynamic programming table, the (back)pointers
and the combined graph of optimal edit transcripts (alignments) computed
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),
text draws the values instead of circles.
The (back)pointers, defining possible (traceback) paths, are plotted
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
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
Some issues with grid were fixed in R.2.4.x (Fixme ?).
D. Gusfield (1997). Algorithms on Strings, Trees, and Sequences. Cambridge University Press, Chapter 11.
Inspired by: http://home.uchicago.edu/~aabbott/.
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