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

In oneillkza/ContiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

Description

ideogramPlot – plots BAIT-like ideograms

Usage

  ## S4 method for signature 'StrandReadMatrix,StrandReadMatrix,ChrTable'
ideogramPlot(WatsonFreqList,
  CrickFreqList, chrTable, plotBy = "lib", sizeProportional = NULL,
  showPage = NULL, 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')
sizeProportional	The plotter will divide each fragment into a discrete number of bins of size sizeProportional and distribute reads across them. For example, when set to 200000, the all contigs in each linkage group will be split into 200kb fragments and each fragment will have an equal proportion of the reads derived from that fragment. This ultimately rescales the ideograms such that LGs with the greatest DNA content are the biggest, as opposed to teh LGs with the most contigs. Default value is NULL
showPage	Integer specifying which LG (if plotBy='chr') or libraries (if plotBy='lib') to plot. Useful when not plotting to a file, or when wishing to subset data. Default is NULL
orderFrame	ordered data.frame of contigs (produced by orderAllLinkageGroups). Default is FALSE, where plots will be made from elements in chrTable.
orientationData	ChrTable of contig orientations 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)

oneillkza/ContiBAIT documentation built on June 1, 2020, 5:49 a.m.