sracipePlotCircuit: Plot Gene Regulatory Circuit

In lusystemsbio/sRACIPE: Systems biology tool to simulate gene regulatory circuits

Plot Gene Regulatory Circuit

Description

Plot Gene Regulatory Circuit to a file or output device using visNetwork. Edge color coding: Transcription-"black", Protein Degradation-"red", Signaling Interaction-"green".

Usage

sracipePlotCircuit(
  .object,
  plotToFile = FALSE,
  physics = TRUE,
  namedNodes = TRUE
)

## S4 method for signature 'RacipeSE'
sracipePlotCircuit(
  .object,
  plotToFile = TRUE,
  physics = TRUE,
  namedNodes = TRUE
)

Arguments

.object	RacipeSE object A list returned by sracipeSimulate function
plotToFile	(optional) logical. Default FALSE. Whether to save plots to a file.
physics	(optional) logical. Default TRUE. Whether or not to enable physics in the nodes of the visNetwork graph.
namedNodes	(optional) logical. Default TRUE. Whether or not to display gene names in the circuit visualization

Value

circuit plot

Related Functions

sracipeSimulate, sracipeKnockDown, sracipeOverExp, sracipePlotData

Examples

data("demoCircuit")
## Not run: 
rSet <- sRACIPE::sracipeSimulate(circuit = demoCircuit, numModels = 20,
integrateStepSize = 0.1, simulationTime = 30)
sracipePlotCircuit(rSet, plotToFile = FALSE, physics = TRUE)
rm(rSet)

## End(Not run)

lusystemsbio/sRACIPE documentation built on Dec. 9, 2024, 8:25 a.m.