simulate_vis {ceRNAnetsim} | R Documentation

## 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)

[Package ceRNAnetsim version 1.2.1 Index]