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).
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])
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(triplex)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rownames, sapply, setdiff, sort, table, tapply, union,
unique, unsplit
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: XVector
Loading required package: Biostrings
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/triplex/triplex.diagram.Rd_%03d_medium.png", width=480, height=480)
> ### Name: triplex.diagram
> ### Title: Triplex visualization, diagram representation
> ### Aliases: triplex.diagram
>
> ### ** Examples
>
> seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
> t <- triplex.search(seq, min_score=10, p_value=1)
Searching for triplex type 0...
Searching for triplex type 1...
Searching for triplex type 2...
Searching for triplex type 3...
Searching for triplex type 4...
Searching for triplex type 5...
Searching for triplex type 6...
Searching for triplex type 7...
> triplex.diagram(t[1])
A DNAStringSet instance of length 4
width seq names
[1] 8 CCCTGCCT minus
[2] 8 GGGACGGA plus
[3] 8 CCTTTCGT para-minus
[4] 5 GGCAT loop
>
>
>
>
>
> dev.off()
null device
1
>