convert2cytoscape: Convert Adjacency Matrix to Cytoscape Format

In SemNeT: Methods and Measures for Semantic Network Analysis

Convert Adjacency Matrix to Cytoscape Format

Description

Converts an adjacency matrix to Cytoscape's sparse matrix format

Usage

convert2cytoscape(A)

Arguments

A	Matrix or data frame. A cleaned, finalized response matrix ready to be visualized

Value

A sparse matrix formatted for Cytoscape

Author(s)

Alexander Christensen <[e-mail]>

References

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., ... & Ideker, T. (2003). Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13, 2498-2504.

Examples

# Simulate Datasets
one <- sim.fluency(10)
two <- sim.fluency(10)

# Compute similarity matrix
cos1 <- similarity(one, method = "cosine")
cos2 <- similarity(two, method = "cosine")

# Compute networks
net1 <- TMFG(cos1)
net2 <- TMFG(cos2)

# Convert to Cytoscape format
cyto1 <- convert2cytoscape(net1)
cyto2 <- convert2cytoscape(net2)

# Write to .csv
write.csv(cyto1, file.path(tempdir(), "cyto1.csv"), row.names = FALSE)
write.csv(cyto2, file.path(tempdir(), "cyto2.csv"), row.names = FALSE)

SemNeT documentation built on Aug. 12, 2023, 5:06 p.m.