plotTree: Plot a dendrogram of the organisms in a pangenome

In FindMyFriends: Microbial Comparative Genomics in R

Description

This method plots a dendrogram of the relationship between the organisms in the pangenome. It does not tries to by phylogenetic in any way but merely shows the relationship in data. As with plotSimilarity it can be based on either the pangenome matrix or kmer feature vectors.

Usage

plotTree(object, ...)

## S4 method for signature 'pgVirtual'
plotTree(object, type = "pangenome",
  circular = FALSE, info, kmerSize, dist, clust, pParam,
  chunkSize = 100)

Arguments

object	A pgVirtual subclass
...	Parameters to be passed on.
type	The type of distance meassure. Either 'pangenome' or 'kmer'
circular	logical. Should the dendrogram be plotted in a circular fashion.
info	Metadata to plot at the leafs of the dendrogram. Either the name of an orgInfo column or a vector with information for each organism.
kmerSize	The size of the kmers to use for comparison
dist	The distance function to use. All possible values of method in dist() are allowed as well as 'cosine' for type='kmer'
clust	The clustering function to use. Passed on to method in hclust()
pParam	An object of class BiocParallelParam
chunkSize	Number of organisms to process at a time

Value

This function is called for its side effects

Methods (by class)

• pgVirtual: Dendrogram plotting for pgVirtual subclasses

See Also

plotSimilarity for a heatmap plot of the same data.

Examples

testPG <- .loadPgExample(withGroups=TRUE)

plotTree(testPG, type='pangenome', dist='binary', clust='ward.D2')

# And now in a circle (type defaults to 'pangenome')
plotTree(testPG, circular=TRUE, dist='binary', clust='ward.D2')

FindMyFriends documentation built on Nov. 8, 2020, 6:46 p.m.