triplex.diagram {triplex} | R Documentation |
This function visualizes a TriplexViews
object as a 2D diagram.
Nucleotides are drawn as characters in circles and bonds as lines between
them (Watson-Crick or Hogsteen).
triplex.diagram(triplex, circles = TRUE, mbonds.lty = 1, mbonds.lwd = 2.5, wcbonds.lty = 1, wcbonds.lwd = 1, hbonds.lty = 2, hbonds.lwd = 1, labels.cex = 1, circles.cex = 1, margin = 0.1, bonds.length = 0.07)
triplex |
|
circles |
TRUE or FALSE: TRUE - nucleotides are drawn as characters in circles, FALSE - nucleotides are drawn just as characters. |
mbonds.lty |
Type of main (skelet) bonds lines. |
mbonds.lwd |
Width of main (skelet) bonds lines. |
wcbonds.lty |
Type of Watson-Crick bonds lines. |
wcbonds.lwd |
Width of Watson-Crick bonds lines. |
hbonds.lty |
Type of Hoogsteen bonds lines. |
hbonds.lwd |
Width of Hoogsteen bonds lines. |
labels.cex |
Multiplier of size of labels of nucleotides. |
circles.cex |
Multiplier of size of nucleotides. |
margin |
Left and right margin of the picture. |
bonds.length |
Length of lines representing Watson-Crick and Hoogsteen bonds. |
The input TriplexViews
object is required to provide additional
algorithm options (see triplex.search
). These are used for
proper computation of triplex alignment.
An example of a graphical output corresponding to a triplex of type 3 with DNA sequence "GGAAAGCAATGCCAGGCAGGG" is shown in the following figure
Instance of DNAStringSet
object with computed alignment.
Kamil Rajdl, Jiri Hon
triplex.3D
,
triplex.search
,
triplex.alignment
seq <- DNAString("GGAAAGCAATGCCAGGCAGGG") t <- triplex.search(seq, min_score=10, p_value=1) triplex.diagram(t[1])