PlotNetwork: Plot the networks, using different colors for transcription...

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

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

Description

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

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.