plotGroup

plotGroup,pgVirtual-method

object

Parameters to be passed on to igraphs plotting method

group

The kmer size to use for similarity calculations

kmerSize

The lower threshold for similarity below which it will be
set to 0

lowerLimit

logical. Should the similarity be rescaled between lowerLimit
and 1

rescale

A transformation function to apply to the similarities

transform


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


A framework for doing microbial comparative genomics in R.
The main purpose of the package is assisting in the creation of
pangenome matrices where genes from related organisms are
grouped by similarity, as well as the analysis of these data.
FindMyFriends provides many novel approaches to doing pangenome
analysis and supports a gene grouping algorithm that scales
linearly, thus making the creation of huge pangenomes feasible.

Thomas Pedersen

FindMyFriends

Microbial Comparative Genomics in R

plotGroup function

<ul>
<li> <code>pgVirtual</code>: Gene group similiarity plotting for all pgVirtual
subclasses
</li>
</ul>

Methods (by class)

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

plotGroup: Plot the similarities of genes within a group

Description

Usage

Arguments

Value

Methods (by class)

Examples