PlotPathComparison.R

PlotPathComparison.R

PlotPathComparison.R is a script to create a plot comparing two paths or attractors. It attempts to align the two attractors to maximize overlap before plotting one attractor blue and the other red, with purple representing the overlap of the two.

Running

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

Parameters should be set in a config file (PlotPathComparison.R /path/to/config.R, see below for config file format).

Parameters

• kboolnetPath: Root directory of the kboolnet repository
• pathA: First of the two paths to be compared.
• pathB: Second of the two paths to be compared.
• path: Indicate that input files are paths, not attractors. This slightly changes how alignment is performed. [default: FALSE]
• nodes: Comma-separated ordered list of nodes to be displayed in the plot. [default: all nodes]
• out: Base name for output files. [default: ./combined]
• nodomains: Remove domains from the output plot? [default: FALSE]

Config file

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

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

Output

Output files will be written based on the out parameter, which is by default ./combined.

• ./combined_all.pdf: Plot of all nodes specified in the nodes parameter.
• ./combined_diff.pdf: Plot of only the nodes that had differences in the two attractors and were specified in the nodes parameter.