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

Description Usage Arguments Details Value Examples

View source: R/simulate_vis.R

Description

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

Usage

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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

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# 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 Nov. 27, 2020, 1:27 a.m.