barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method: Bar plot all linkage groups, with the true chromosomes of...

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

Description

Bar plot all linkage groups, with the true chromosomes of contigs coloured.

Usage

## S4 method for signature 'LinkageGroupList,ChrTable'
barplotLinkageGroupCalls(object, chrTable,
  by = "lg", bySize = TRUE, returnTable = NULL, whichGroup = NULL,
  percentage = NULL)

Arguments

object	LinkageGroupList, as generated by clusterContigs
chrTable	GRanges object containing assembly information about the contigs, including a meta column called 'name' that has names matching the object. Note that the rownames of chrTable should be the contig names, as they are used in object, and the first column (chromosome name) will used to order by chromosome if 'chr' option used in by parameter. To use a bam file header, the product of makeChrTable(bamFile) is suitable for input
by	whether to plot by linkage group (if 'lg') or chromosomes ('chr')
bySize	logical value to return barplot either with LGs sorted by number of contigs or size (in Mb). Default is TRUE.
returnTable	Logical to return chromosome length matrix. Default is NULL
whichGroup	Numeric vector of groups to analyse. If by='lg', then only the subset of LGs selected by whichGroup will be analyzed. If by='chr', then only subset of chromosomes selected by whichGroup will be analyzed. Note to include legend, use legend=rownames(chr.table) for by='lg', and legend=colnames(chr.table) for by='chr'
percentage	Logical that returns the percentage of different chromosomes or LG within the barplot. Default is NULL

Value

a matrix of lengths of each chromosome (rows) in each linkage group (columns)

Examples

data("exampleLGList")
data("exampleDividedChr")

barplotLinkageGroupCalls(exampleLGList, exampleDividedChr)

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