plotSimilarity: Create a heatplot with similarities between all organisms

In thomasp85/FindMyFriends: Microbial Comparative Genomics in R

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

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

testPG <- .loadPgExample(withGroups=TRUE)

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

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

thomasp85/FindMyFriends documentation built on April 25, 2020, 1:06 p.m.