BTR (version 1.2.4)

outstate_graph: Generate state transition graph

Description

This function generates a state transition graph using a Boolean model and its state space. Each node represent a state. All nodes in this graph is linked by an edge only if the 2 states have different value in only 1 gene. The output is readable by Cytoscape and Gephi.

Usage

outstate_graph(mstate, bmodel, directed = F, record.both = F, filepath = getwd())

Arguments

mstate

data frame. It should be a state(row) x gene(column) df.

bmodel

S4 BoolModel object.

directed

logical. Indicates whether to make directed edges or not. Default to FALSE.

record.both

logical. Indicates whether to also record nodes that have no edges. Default to FALSE.

filepath

character vector. Specify path (AND NOT file name). Default to current working directory, i.e. getwd(). Set to NULL to disable file output.