plotLGDistances,LinkageGroupList,StrandStateMatrix-method {contiBAIT} | R Documentation |
plotLGDistances – plots a heatmap of the distances between linkage groups
## S4 method for signature 'LinkageGroupList,StrandStateMatrix' plotLGDistances(object, allStrands, lg = "all", labels = TRUE, state = "all", alreadyOrdered = FALSE)
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 |
a heatplot of linkage group calls
data("exampleLGList") data("exampleWCMatrix") plotLGDistances(exampleLGList, exampleWCMatrix) plotLGDistances(exampleLGList, exampleWCMatrix, lg=1)