create_cytoscape_file: Create an edge table file for Cytoscape

In tgrimes/SeqNet: Generate RNA-Seq Data from Gene-Gene Association Networks

Description

The returned data frame can be saved as a .csv file. Then, in Cytopscape use File -> Import -> Network -> File. Select the .csv file containing the data frame generated by this function. There will be a popup window. The source, interaction, and target columns should automatically be identified. Click OK.

Usage

create_cytoscape_file(g)

Arguments

g	A 'network_plot' object. See ?plot_network().

Examples

nw <- random_network(10)
g <- plot(nw)
nw_plot_cytoscape <- create_cytoscape_file(g)

# Save the edge table in a .csv file to be used in cytoscape.
write.table(nw_plot_cytoscape, file.path(tempdir(), "file_name.csv"), 
            sep = ",", row.names = FALSE, col.names = TRUE, quote = FALSE)

tgrimes/SeqNet documentation built on Sept. 1, 2020, 7:50 a.m.