Create a heatplot with similarities between all organisms

Description

This method creates a heatplot showing the similarity between all organisms in the pangenome. The similarity can either be derived from the pangenome matrix or from kmer calculations of the genes themselves.

Usage

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plotSimilarity(object, ...)

## S4 method for signature 'pgVirtual'
plotSimilarity(object, type = "pangenome",
  ordering = "auto", kmerSize, pParam, chunkSize = 100)

Arguments

object

A pgVirtual subclass

...

Parameters to be passed on.

type

The type of similarity calculation. Either 'pangenome' or 'kmer'

ordering

The ordering of rows and column in the heatmap. Either integer og character vector with organism names or one of the following: 'auto' or 'none'. For 'auto' The ordering will be based on a hierarchical clustering of the organisms based on Ward's distance.

kmerSize

The size of the kmers to use for comparison

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: Similarity heatmaps for pgVirtual subclasses

See Also

plotTree for a dendrogram plot of the same data.

Examples

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testPG <- .loadPgExample(withGroups=TRUE)

# Use kmers
plotSimilarity(testPG, type='kmer')

# Use pangenome matrix
plotSimilarity(testPG, type='pangenome')

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