plotLGDistances-LinkageGroupList-StrandStateMatrix-method: plotLGDistances - plots a heatmap of the distances between...

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

Description

plotLGDistances – plots a heatmap of the distances between linkage groups

Usage

## S4 method for signature 'LinkageGroupList,StrandStateMatrix'
plotLGDistances(object,
  allStrands, lg = "all", labels = TRUE, state = "all",
  alreadyOrdered = FALSE)

Arguments

object	LinkageGroupList
allStrands	StrandStateMatrix for all linkageGroups (usually reoriented by reorientStrandTable)
lg	='all' vector of integers to determine which linkage group(s) to plot. 'all' will calculate consensus strand calls for all linkage groups and plot them side by side (default it 'all')
labels	=TRUE if TRUE, contig names will be plotted on the axes
state	string denoting whether only homozygous states should be used ('homo'; just WW vs CC), if a comparison should be made between homozygous and heterozygous states only ('hetero'; just homo vs hetero), or if all three states ('all'; WW vs WC vs CC). Default is 'all'
alreadyOrdered	if TRUE, the function will assume that the linkageGroupList is already ordered and not create a dendrogram. Default is FALSE
...	additional parameters to pass to heatmap.2

Value

a heatplot of linkage group calls

Examples

data("exampleLGList")
data("exampleWCMatrix")

plotLGDistances(exampleLGList, exampleWCMatrix)
plotLGDistances(exampleLGList, exampleWCMatrix, lg=1)

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