sismonr (version 2.1.0)

plotGRN: Plots the GRN of the in silico system.

Description

Plots the gene regulatory network of the insilico system, including all types of regulation or only those defined by the user.

Usage

plotGRN(
  insilicosystem,
  edgeType = NULL,
  showAllVertices = F,
  plotType = "2D",
  ...
)

Arguments

insilicosystem

The in silico system (see createInSilicoSystem).

edgeType

The type of interactions to plot. If NULL (default value), all the interactions are plotted. Otherwise, can be either:

• "TC": plot only regulation of transcription

• "TL": plot only regulation of translation

• "RD": plot only regulation of RNA decay

• "PD": plot only regulation of protein decay

• "PTM": plot only regulation of protein post-translational modification

• "RegComplexes": plot only binding interactions, i.e. linking the regulatory complexes to their components.

showAllVertices

Display vertices that don't have any edge? Default is FALSE

plotType

The type of plot function to use for the network: can be either "2D" (default, use the function plot.igraph) or "interactive2D" (use the function tkplot).

...

any other arguments to be passed to the plot function, see igraph.plotting.

Examples

# NOT RUN {
mysystem = createInSilicoSystem(G = 10)
plotGRN(mysystem)
plotGRN(mysystem, edgeType = "TC")
plotGRN(mysystem, edgeType = "TC", showAllVertices = T)
# }