visPandaInCytoscape: Plot PANDA network in Cytoscape

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Plot PANDA network in Cytoscape

Description

This function is able to modify PANDA network and plot in Cytoscape. Please make sure that Cytoscape is installed and open it before calling this function.

Usage

visPandaInCytoscape(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.

Value

PANDA network in Cytoscape

Examples

# refer to the input datasets files of control TB dataset in inst/extdat as example
control_expression_file_path <- system.file("extdata", "expr10_matched.txt", 
package = "netZooR", mustWork = TRUE)
motif_file_path <- system.file("extdata", "chip_matched.txt", package = "netZooR", mustWork = TRUE)
ppi_file_path <- system.file("extdata", "ppi_matched.txt", package = "netZooR", mustWork = TRUE)

# Run PANDA algorithm
control_all_panda_result <- pandaPy(expr = control_expression_file_path, motif = motif_file_path, 
ppi = ppi_file_path, modeProcess="legacy", remove_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$Score,decreasing = TRUE),], 1000)

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

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.