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Last data update: 2014.03.03

R: ideogramPlot - plots BAIT-like ideograms

ideogramPlot,StrandReadMatrix,StrandReadMatrix,ChrTable-method

R Documentation

ideogramPlot – plots BAIT-like ideograms

Description

ideogramPlot – plots BAIT-like ideograms

Usage


  ## S4 method for signature 'StrandReadMatrix,StrandReadMatrix,ChrTable'
ideogramPlot(WatsonFreqList,
  CrickFreqList, chrTable, plotBy = "lib", showPage = FALSE,
  orderFrame = NULL, orientationData = NULL, verbose = TRUE)

Arguments

`WatsonFreqList`	data.frame of Watson calls. Product of strandSeqFreqTable[[3]] when BAITtables=TRUE
`CrickFreqList`	data.frame of Crick calls. Product of strandSeqFreqTable[[4]] when BAITtables=TRUE
`chrTable`	A data.frame consisting of chromosomes and lengths. Generated by makeChrTable(). Note rownames equal to chromosome names are required
`plotBy`	Whether to generate a plot for each library ('lib') or a plot for each chromosome ('chr')
`showPage`	Integer specifying which page to plot if plotBy='chr' selected. Useful when not plotting to a file. Default is FALSE
`orderFrame`	ordered data.frame of contigs (produced by orderAllLinkageGroups). Default is FALSE, where plots will be made from elements in chrTable.
`orientationData`	data.frame of contig orientations of type OrientationFrame telling which reads to flip Watson and Crick counts
`verbose`	prints messages to the terminal (default is TRUE)

Value

ordered contigs in bed format. Depending on options, intermediate files and plots will also be generated

Examples

data("exampleWatsonFreq")
data("exampleCrickFreq")
data('exampleDividedChr')

singleWatsonLibrary <- StrandReadMatrix(exampleWatsonFreq[,2, drop=FALSE])
singleCrickLibrary <- StrandReadMatrix(exampleCrickFreq[,2, drop=FALSE])

ideogramPlot(singleWatsonLibrary, singleCrickLibrary, exampleDividedChr)

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)

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Type 'q()' to quit R.

> library(contiBAIT)
Loading required package: BH
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/contiBAIT/ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ideogramPlot,StrandReadMatrix,StrandReadMatrix,ChrTable-method
> ### Title: ideogramPlot - plots BAIT-like ideograms
> ### Aliases: ideogramPlot
> ###   ideogramPlot,StrandReadMatrix,StrandReadMatrix,ChrTable-method
> ###   ideogramPlot,StrandReadMatrix,StrandReadMatrix-method,ChrTable,ChrTable-method
> 
> ### ** Examples
> 
> data("exampleWatsonFreq")
> data("exampleCrickFreq")
> data('exampleDividedChr')
> 
> singleWatsonLibrary <- StrandReadMatrix(exampleWatsonFreq[,2, drop=FALSE])
> singleCrickLibrary <- StrandReadMatrix(exampleCrickFreq[,2, drop=FALSE])
> 
> ideogramPlot(singleWatsonLibrary, singleCrickLibrary, exampleDividedChr)
-> Generating plotting data [1/1]
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>