triplex.diagram: Triplex visualization, diagram representation

In triplex: Search and visualize intramolecular triplex-forming sequences in DNA

Description

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).

Usage

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)

Arguments

triplex	TriplexViews object including only one 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.

Details

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

Value

Instance of DNAStringSet object with computed alignment.

Author(s)

Kamil Rajdl, Jiri Hon

See Also

triplex.3D, triplex.search, triplex.alignment

Examples

seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
t <- triplex.search(seq, min_score=10, p_value=1)
triplex.diagram(t[1])

triplex documentation built on Nov. 8, 2020, 5:34 p.m.