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.
vis.panda.in.cytoscape(panda.net, network_name = "PANDA")
panda.net | Character string indicating the input PANDA network in data frame structure type. |
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network_name | Character string indicating the name of Cytoscape network. |
PANDA network in Cytoscape
if (FALSE) { # 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 <- panda.py(expr = 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$panda # select top 1000 edges in PANDA network by edge weight. panda.net <- head(control_net[order(control_net$force,decreasing = TRUE),], 1000) # run this function to create a network in Cytoscape. vis.panda.in.cytoscape(panda.net, network.name="PANDA") }