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Last data update: 2014.03.03

R: Plot metaprofiles of DNA shape features

plotShape

R Documentation

Plot metaprofiles of DNA shape features

Description

DNA shape features can be visualized as aggregated line plots (also known as metaprofiles, see Comoglio et al., 2015), heat maps (Yang et al., 2014) and genome browser tracks (Chiu et al., 2014).

Usage

plotShape(shapeMatrix, background = NULL,
colDots = rgb( 0, 0, 1, 0.1),
colDotsBg = rgb( 0, 0, 0, 0.1),
colLine = 'steelblue', colLineBg = 'gray50', cex = 0.5, lwd = 2, ylim, ...)

Arguments

`shapeMatrix`	A matrix containing DNAshape prediction results
`background`	A matrix containing DNAshape prediction results for a set of background regions. Default to NULL, i.e. background not provided.
`colDots`	A character vector specifying the color of the points representing the column mean of shapeMatrix. Default to rgb( 0, 0, 1, 0.1).
`colDotsBg`	A character vector specifying the color of the points representing the column mean of background. Default to rgb( 0, 0, 0, 0.1).
`colLine`	A character string giving the color name of line representing the column mean of shapeMatrix. Default to 'steelblue'.
`colLineBg`	A character string giving the color name of line representing the column mean of background. Default to 'gray50'.
`cex`	A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. Default to 0.5.
`lwd`	A numerical value specifying the line width. Default to 2.
`ylim`	A numerical vector of size 2 specifying the y-axis plot range.
`...`	Additional parameters to be passed to the R plot function.

Value

Called for its effects

Author(s)

Federico Comoglio

Examples

fn <- system.file("extdata", "CGRsample.fa", package = "DNAshapeR")
pred <- getShape(fn)
plotShape(pred$MGW)
plotShape(pred$ProT)
plotShape(pred$Roll)
plotShape(pred$HelT)

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(DNAshapeR)
Loading required package: GenomicRanges
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

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DNAshapeR/plotShape.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotShape
> ### Title: Plot metaprofiles of DNA shape features
> ### Aliases: plotShape
> ### Keywords: core
> 
> ### ** Examples
> 
> fn <- system.file("extdata", "CGRsample.fa", package = "DNAshapeR")
> pred <- getShape(fn)
Reading the input sequence......
Reading the input sequence......
Reading the input sequence......
Reading the input sequence......
Parsing files......
Read 34000 items
Record length: 2000
Read 34000 items
Record length: 1999
Read 34000 items
Record length: 2000
Read 34000 items
Record length: 1999
Done
> plotShape(pred$MGW)
> plotShape(pred$ProT)
> plotShape(pred$Roll)
> plotShape(pred$HelT)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>