plotGroup: Plot the similarities of genes within a group

In FindMyFriends: Microbial Comparative Genomics in R

Description

This method plots a gene group with genes as vertices and cosine similarities as weighted edges. Mildly informative at best :-)

Usage

plotGroup(object, ...)

## S4 method for signature 'pgVirtual'
plotGroup(object, group, kmerSize, lowerLimit,
  rescale, transform, ...)

Arguments

object	A pgVirtual subclass
...	Parameters to be passed on to igraphs plotting method
group	Name or index of the gene group to plot
kmerSize	The kmer size to use for similarity calculations
lowerLimit	The lower threshold for similarity below which it will be set to 0
rescale	logical. Should the similarity be rescaled between lowerLimit and 1
transform	A transformation function to apply to the similarities

Value

Called for the side effect of creating a plot. Invisibly returns an igraph object with all visual parameters set as node and edge attributes.

Methods (by class)

• pgVirtual: Gene group similiarity plotting for all pgVirtual subclasses

Examples

testPG <- .loadPgExample(withGroups=TRUE)

plotGroup(testPG, 10, lowerLimit=0.25)

FindMyFriends documentation built on Nov. 8, 2020, 6:46 p.m.