plotLGDistances,LinkageGroupList,StrandStateMatrix-method {contiBAIT} | R Documentation

## plotLGDistances – plots a heatmap of the distances between linkage groups

### 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)

[Package contiBAIT version 1.15.0 Index]