RNAPlot {RRNA}

Generic RNA Secondary Structure Plotting Function

Description

Given fold data from loadFolds or ct2coords RNAPlot plots the secondary structure

Usage

RNAPlot(data, 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 = "", pointSize = 2, lineWd = 2)

Arguments

data

R data frame containing the coordinates for plotting a given secondary structure ### Example input file format: ### ### 0,158.534088,199.550888,G,0,-1 ### 0,152.741776,194.100571,A,1,-1 ### 0,149.307266,186.849899,A,2,-1 ### 0,148.749847,178.776566,G,3,-1 ### 0,151.196960,170.989944,C,4,59 ### 0,141.412643,159.620361,U,5,58 ### 0,131.628342,148.250793,U,6,57 ### 0,121.844025,136.881210,A,7,56 ### 0,112.059715,125.511642,C,8,55 ### 0,102.275398,114.142059,A,9,54 ### 0,89.142853,109.343330,A,10,-1 ### .... ### ### There is no header on the input file. The columns are ### ID,X,Y,SEQ,POS,BOUND ### ### ID - A unique ID for a given fold in the file ### X - X position of the NT in the secondary structure plot ### Y - Y position of the NT in the secondary structure plot ### SEQ - The nucleotide (A,G,U,C) ### POS - The position of the NT in the sequence ### BOUND - The position of the NT that the NT at POS is bound to

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.

pointSize

The size of points plotted in the secondary structure. Values betwen 0.1-5 work well.

lineWd

Line width for base pairings and backbone of secondary structures.

Value

Returns a generic R plot that can be used with the jpeg, postscript, etc. functions.

Author(s)

JP Bida

See Also

makeCt,loadCoords,ct2coord

Examples

## Create a CT file from bracket notation and sequence ###
ct=makeCt( "((((...(((((((....)))))))...((((...))))...))))",
          "CCCCAAAGGGGGGGAUUACCCCUCCUUUAAAAGGGUUUUCCCCCCC"
)

## Create a coordinate file based on the CT file ###
dat=ct2coord(ct)

### Create a plot of the secondary structure ###
RNAPlot(dat)

### Plot positions 1:4 as green and 43:46 circles ## 
### and show the legend
ranges=data.frame(min=c(1,43),max=c(4,46),col=c(2,3),
                  desc=c("Region 1","Region 2")
                 )
RNAPlot(dat,ranges,labTF=TRUE)

### Highlight the sequences CUCCU and CCCCAAA ###

RNAPlot(dat,hl=c("CUCCU","CCCCAAA"),seqcol=c(2,4),labTF=TRUE,main="RNA Molecule")

### Modify specific positions ####

RNAPlot( dat, modspec=TRUE, modp=c(1:4,43:46),mod=c(17,17,15,15,16,16,16,16),
         modcol=c(rep(2,2),rep(3,2),rep(4,4))
       )

### RNA Plot with nucleotides ###
RNAPlot(dat,nt=TRUE)

### RNA plot with nucleotides
RNAPlot( dat,nt=TRUE,modspec=TRUE,modp=c(1:4,43:46),
         mod=c(17,17,15,15,16,16,16,16),
         modcol=c(rep(2,2),rep(3,2),rep(4,4))
       )

### RNA Plot wiht nucleotides and dots ###

RNAPlot(dat)
RNAPlot(dat,nt=TRUE,add=TRUE,dp=0.75)