plotLGDistances – plots a heatmap of the distances between linkage groups

Description

plotLGDistances – plots a heatmap of the distances between linkage groups

Usage

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

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

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