simulate_vis: Provides visualisation of the graph in addition to simulate...

In selcenari/ceRNAnetsim: Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)

Provides visualisation of the graph in addition to simulate function.

Description

simulate_vis provides visualisation of the graph in addition to simulate function.

Usage

simulate_vis(
  input_graph,
  cycle = 1,
  threshold = 0,
  save = FALSE,
  Competing_color = "green",
  mirna_color = "orange",
  Upregulation = "red",
  Downregulation = "blue",
  title = "GRAPH",
  layout = "kk"
)

Arguments

input_graph	The graph object that processed in previous steps.
cycle	Optimal iteration number for gaining steady-state.
threshold	absolute minimum amount of change required to be considered as up/down regulated element
save	provides to save graph output
Competing_color	The color of competing elements on the graph with "green" default.
mirna_color	The color of miRNAs on the graph with "orange" default.
Upregulation	The color of Upregulated elements on the graph with "red" default.
Downregulation	The color of Downregulated elements on the graph with "blue" default.
title	Title of the given graph.
layout	The layout that will be used for visualisation of the graph.

Details

simulate_vis gives the last graph object and each iterations' image.

Value

It gives a graph and the images of states in each iteration until the end of the simulation.

Examples

# When does the system gain steady-state conditions again?

## new_counts, the dataset that includes the current counts of nodes.

data("minsamp")
data("new_counts")

priming_graph(minsamp, Competing_expression, miRNA_expression)%>%
  update_variables(new_counts)%>%
  simulate_vis()

priming_graph(minsamp, Competing_expression, miRNA_expression, 
    aff_factor = c(seed_type,energy), deg_factor = c(region))%>%
  update_variables(new_counts)%>%
  simulate_vis(cycle = 12)

selcenari/ceRNAnetsim documentation built on Feb. 14, 2024, 4:20 a.m.