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

Description Usage Arguments Value Examples

Description

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

Usage

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## 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

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

barplotLinkageGroupCalls(exampleLGList, exampleDividedChr)

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