plotBipartiteSummary: Function to plot a bipartite graph to summarise strain-strain...
In cmfield/phylloR: R package for phyllosphere analysis

plotBipartiteSummary

R Documentation

Function to plot a bipartite graph to summarise strain-strain interactions.

Description

Function to plot a bipartite graph to summarise strain-strain interactions.

Usage

plotBipartiteSummary(fcMatrix, pvMatrix, leftPhylo = NULL,
  rightPhylo = NULL, leftOrder = NULL, rightOrder = NULL,
  leftLabs = NULL, rightLabs = NULL, leftCols = NULL,
  rightCols = NULL, leftScale = 1, rightScale = 1,
  experiment.type = "removal", tip.label.width = 0.1, cutoff = 0.05)

Arguments

`fcMatrix`	A matrix of fold changes where the rows are labelled with the affected strains and the columns with the affector strains.
`pvMatrix`	A matrix of p-values matching "fcMatrix".
`leftPhylo`	An optional phylo object describing the phylogeny of the affector strains.
`rightPhylo`	An optional phylo object describing the affected strains.
`leftOrder`	An optional vector of character strings to place the affector strains in a particular order.
`rightOrder`	An optional vector of character strings to place the affected strains in a particular order.
`leftLabs`	An optional vector of character strings to label the affector strains.
`rightLabs`	An optional vector of character strings to label the affected strains.
`leftCols`	An optional vector of colors for the affector strain labels.
`rightCols`	An optional vector of colors for the affected strain labels.
`experiment.type`	A character string that is either "removal" or "addition" to describe the nature of the perturbations to the core experiment.
`tip.label.width`	A numeric to indicate how much space should be placed between the tips of the tree (if provided) and graph lines.
`cutoff`	A numeric to specify a p-value cutoff above which lines will not be plotted.