plotPANDAinCytoscape: Plot PANDA network in Cytoscape

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

Description

This function is able to modify PANDA network and plot in Cytoscape.

Usage

plotPANDAinCytoscape(panda.net, network.name = "PANDA")

Arguments

panda.net	Character string indicating the input PANDA network in data frame structure type.
network.name	Character string indicating the name of Cytoscape network.

Examples

# refer to the input datasets files of control TB dataset 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

# select top 1000 edges in PANDA network by edge weight.
panda.net <- head(control_net[order(control_net$force,decreasing = T),], 1000)

# run this function to create a network in Cytoscape.
plotPANDAinCytoscape(panda.net, network.name="PANDA")

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