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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.


visPandaInCytoscape(, network_name = "PANDA")


Character string indicating the input PANDA network in data frame structure type.


Character string indicating the name of Cytoscape network.


PANDA network in Cytoscape


# \donttest{
# 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 <- = control_expression_file_path, motif = motif_file_path, 
ppi = ppi_file_path, mode_process="legacy", rm_missing = TRUE )

# access PANDA regulatory network
control_net <- control_all_panda_result$panda

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

# run this function to create a network in Cytoscape.
# }