Description Usage Arguments Value Methods (by class) See Also Examples
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.
1 2 3 4 5 | plotSimilarity(object, ...)
## S4 method for signature 'pgVirtual'
plotSimilarity(object, type = "pangenome",
ordering = "auto", kmerSize, pParam, chunkSize = 100)
|
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 |
This function is called for its side effects
pgVirtual
: Similarity heatmaps for pgVirtual subclasses
plotTree
for a dendrogram plot of the same data.
1 2 3 4 5 6 7 | testPG <- .loadPgExample(withGroups=TRUE)
# Use kmers
plotSimilarity(testPG, type='kmer')
# Use pangenome matrix
plotSimilarity(testPG, type='pangenome')
|
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