Plot the networks, using different colors for transcription factors, genes of interest, and additional genes.

Usage

PlotNetwork(
  network,
  genesOfInterest,
  tfColor = "blue",
  nodeSize = 1,
  edgeWidth = 0.5,
  vertexLabels = NA,
  vertexLabelSize = 0.7,
  vertexLabelOffset = 0.5,
  layoutBipartite = TRUE,
  geneColorMapping = NULL
)

Arguments

network: A data frame with the following format: tf,gene
genesOfInterest: Which genes of interest to highlight
tfColor: Color for the transcription factors
nodeSize: Size of node
edgeWidth: Width of edges
vertexLabels: Which vertex labels to include. By default, none are included.
vertexLabelSize: The size of label to use for the vertex, as a fraction of the default.
vertexLabelOffset: Number of pixels in the offset when plotting labels. Default is TRUE.
layoutBipartite: Whether or not to layout as a bipartite graph.
geneColorMapping: Color mapping from a set of genes to a color. The nodes and edges connected to them will be this color. If NULL, all genes and their edges will be gray. The format is a data frame, where the first column ("gene") is the name of the gene and the second ("color") is the color.

Value

A bipartite plot of the network