plotTree {FindMyFriends} | R Documentation

## 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, ...)

    ## 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')

[Package FindMyFriends version 1.16.0 Index]