contiBAIT (version 1.0.0)

ideogramPlot,StrandReadMatrix,StrandReadMatrix,ChrTable-method: ideogramPlot -- plots BAIT-like ideograms

Description

ideogramPlot -- plots BAIT-like ideograms

Usage

## S3 method for class '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)