FindMyFriends (version 1.2.2)

plotTree: Plot a dendrogram of the organisms in a pangenome

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, ...)
"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')