contiBAIT (version 1.0.0)

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

Description

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

Usage

## S3 method for class 'LinkageGroupList,ChrTable':
barplotLinkageGroupCalls(object, chrTable,
  by = "lg", returnTable = FALSE)

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')

returnTable

TRUE to return chromosome length matrix. Note to include legend, use legend=rownames(chr.table) for by='lg', and legend=colnames(chr.table) for by='chr'

Value

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

Examples

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

barplotLinkageGroupCalls(exampleLGList, exampleDividedChr)