aptPlotCT {RRNA}

RNA secondary structure plotting from CT files

Description

Generates and RNA secondary structure plot from a CT file. Removes pseudoKnots automatically and allows them to be drawn back in with pseudoTF=TRUE.

Usage

aptPlotCT(file, ranges = 0, add = FALSE, hl = NULL, seqcols = NULL,
          seqTF = FALSE, labTF = FALSE, nt = FALSE, dp = 0.5, 
          modspec = FALSE, modp = NULL, mod = NULL, modcol = NULL, 
          tsize = 0.5, main = "", pseudoTF = FALSE, pseudo_nums = NULL, 
          ticks = NULL, ticksTF = FALSE
         )

Arguments

file

CT file name

ranges

A data frame containing the ranges of sequence positions that should be highlighted with given colors. ranges=data.frame(min=c(69,1,7),max=c(74,5,17),col=c(2,3,4),desc=c("Region 1","Region 2","Region 3")) The above will highlight the nucleotides at positions 69-74, 1-5, and 7-17 respectively

add

Should the new plot be added to an existing plot TRUE/FALSE

hl

Takes an array of sequences and highlights them with seqcol hl=c("GGGAAAA","GGGCCCC") The above hl will highlight the nucleotides in the secondary structure that have the given sequences with the colors provided in the seqcols option.

seqcols

Colors that should be used to highlight the sequences given in hl

seqTF

If sequence is a vector set as TRUE

labTF

TRUE/FALSE plot the legend

nt

TRUE/FALSE plot the nucleotide sequence on the secondary structure

dp

Floating point value to determine how far from the coordinates the nucleotide sequence should be plotted. Values between 0 and 5 usually work best.

modspec

TRUE/FALSE modify specific positions in the secondary structure. Used in combination with modp,mod,and modcol. This allows you to change the shape and color of nucleotide in the secondary structure.

modp

Array defining the specific positions to be modified in the plot modp=c(1:10)

mod

Array defining the pch values to be plotted at the positions given by modp. mod=c(rep(15,5),rep(16,5))

modcol

Array of color values to be used for plotting at the positions defined by modp in the secondary structure. modcol=rep(4,10)

tsize

Text size used for plotting the nucleotide sequence in the secondary structure. Only applicable when nt=TRUE. Values between 0.1 and 4 work well.

main

Title used for the plot when labTF is set to TRUE.

pseudoTF

Plot pseudo knot sequences

pseudo_nums

indices of the nucleotides included in pseudoknots

ticksTF

TRUE/FALSE include ticks

ticks

Positions where the ticks should be drawn. These are sequence positions in the RNA molecule

Value

Returns and R plot object

Author(s)

JP Bida

See Also

RNAPlot

Examples

### PseudoKnots ###
pk= makeCt("((((...(((((((.........)))))))...((((.........))))...))))",
          "AAAAAAAACCCCCCCCAAAGGGGGGGAUUACCCCUCCUUUAAAAGGGUUUUCCCCCCC"
         )
pk$bound[pk$pos==20]=42
pk$bound[pk$pos==19]=43
pk$bound[pk$pos==43]=19
pk$bound[pk$pos==42]=20
f = tempfile()
### Create a CT file for testing ###
write.table(pk[,c(1,4,2,3,6,5)],file=f,row.names=FALSE,col.names=TRUE)

aptPlotCT(f,ticksTF=TRUE,ticks=seq(1,60,by=5),pseudoTF=TRUE,pseudo_nums=c(19,20,43,42))