TruthTable.R

TruthTable.R

TruthTable.R is a script that creates a table showing the behavior of a given model under all possible combinations of certain inputs and inhibitors.

Running

Run TruthTable.R by sourcing it directly (./TruthTable.R) or with Rscript (Rscript ./TruthTable.R).

Parameters can be set as command-line arguments (TruthTable.R --arg="value") or in a config file (TruthTable.R --config="/path/to/config.R", see below for config file format). Command-line arguments override parameters set in the config file.

Parameters

• kboolnetPath: Root directory of the kboolnet repository
• file: Path of local master rxncon file
• nodes: Comma-separated list of nodes to be displayed in the plot. [default: all nodes]
• out: Name of PDF file to which plot should be written. [default: ./plot.PDF]
• nodomains: Remove domains from the output plot? [default: FALSE]
• ratio: Width:height ratio of the tiles in the graph. [default: 0.8]

Config file

Config files should be .R files following this general format:

config <- list(
	arg1 = "string value",
	arg2 = FALSE,
	arg3 = 23
	...
)