plotLioness: Plot single-sample network

In twangxxx/netZoo: Integrate methods: PANDA, LIONESS, CONDOR, ALPACA into one workflow.

Description

This function is able to plot sepecified amount of edges in a specified sample network. This function should be used following the runLioness. As LIONESS estimates the single-sample network of an aggregate network generated by PANDA (more )

Usage

plotLioness(col = 0, top = 100, file = "lioness_top_100.png")

Arguments

col	Numerical Vector indicating the index (0-based)of specified sample in a population. Defaults to 0.
top	Numeric Vector indicating the amount of edges selected to plot by decreasting order of egde weights. Defaults to 100.
file	Character String indicating the name of output .png file. Defaults to 'lioness_top_100.png'.

Value

A message showing the path of output plot.

Examples

# refer to the input datasets files of control in inst/extdat as example
control_expression_file_path <- system.file("extdata", "expr10.txt", package = "netZoo", mustWork = TRUE)
motif_file_path <- system.file("extdata", "chip.txt", package = "netZoo", mustWork = TRUE)
ppi_file_path <- system.file("extdata", "ppi.txt", package = "netZoo", mustWork = TRUE)

# Run PANDA algorithm
control_lioness_result <- runLioness(e = control_expression_file_path, m = motif_file_path, ppi = ppi_file_path, rm_missing = TRUE )

# plot the top 100 egdes in first sample network.
plotLioness(col = 0, top = 100, file = "top100_sample1.png")

twangxxx/netZoo documentation built on May 17, 2019, 1:02 p.m.