SteinerNet (version 3.1.0)

steiner_comparison_plots: Plot simulated data

Description

This function plots the comparison results of simulated data and stores it in PDF file.

Usage

steiner_comparison_plots(type, method, data, outputname)

Arguments

type

a character vector, which indicates types of algorithms to analyse. Can be "EXA", "SP", "KB", "RSP", "SPM" or "ASP".

method

a character vector; specifies a calculated parameter based on which comparison is performed. Can be "runtime" (for time of execution), "log10runtime", "edge" (for number of edges in resultant steiner tree), "log10edge", "ter_freq" (for terminal frequency in resultant steiner tree) or "edge_dens" (for edge density in resultant steiner tree).

data

should have structure as output of steiner_simulation function.

outputname

a character scalar; name of file in which the result is stored

Value

For each method a plot with comparison of algorithms (pointed in type variable) is created. An additional information about the number of experiments and number of terminals for each type of algorithm is added. If the number of terminals is the same for each type, then their number is printed, otherwise the range is printed.

References

1. Afshin Sadeghi and Holger Froehlich, "Steiner tree methods for optimal sub-network identification: an empirical study", BMC Bioinformatics 2013 14:144

See Also

generate_st_samples, steiner_simulation, steinertree

Examples

# NOT RUN {
g <- graph("Cubical")

data <- steiner_simulation(type = c("SP", "KB", "SPM"),
                           graph = g,
                           ter_list = generate_st_samples(graph = g,
                                                          ter_number = c(2, 3),
                                                          prob = c(0.1, 0.2)))

steiner_comparison_plots(type = c("SP", "KB"),
                         method = c("runtime", "ter_freq"),
                         data = data,
                         outputname = tempfile(pattern = "file", tmpdir = tempdir()))

# }