plotPanda: Plot PANDA network

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

Description

This function is able to plot specified amount of egdes in PANDA network, after generate PANDA network runPanda.

Usage

plotPanda(top = 100, file = "panda_top_100.png")

Arguments

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 'panda_top_100.png'.

Value

a message showing the path of output plot file.

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_all_panda_result <- runPanda(e = control_expression_file_path, m = motif_file_path, ppi = ppi_file_path, rm_missing = TRUE )

# access PANDA regulatory network
control_net <- control_all_panda_result$panda

# plot the top 100 edges of the PANDA network
plotPanda(top =100, file="top100_panda.png")

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