scudoCytoscape: Create a Cytoscape network from the output of scudoNetwork

In Matteo-Ciciani/scudo: Signature-based Clustering for Diagnostic Purposes

Create a Cytoscape network from the output of scudoNetwork

Description

A wrapper to RCy3 function calls to plot the result of scudoNetwork in Cytoscape 3. Cytoscape must be open before running this function.

Usage

scudoCytoscape(graph, title = "Scudo Graph", collection = "SCUDO")

Arguments

graph	object of class igraph, like the result of scudoNetwork
title	the title of the network
collection	the name of the Cytoscape collection

Value

The network SUID (an integer).

Author(s)

Matteo Ciciani [e-mail], Thomas Cantore [e-mail]

See Also

scudoNetwork, RCy3

Examples

# generate dummy dataset
exprData <- data.frame(a = 11:20, b = 16:25,
    c = rev(1:10), d = c(1:2, rev(3:10)))
rownames(exprData) <- letters[11:20]
grps <- as.factor(c("G1", "G1", "G2", "G2"))
nTop <- 2
nBottom <- 3

# run scudoTrain and scudoNetwork
res <- scudoTrain(exprData, grps, nTop, nBottom, foldChange = FALSE,
    featureSel = FALSE)
col <- c("#FF00FF", "#FF00FF", "#00FF00", "#00FF00")
net <- scudoNetwork(res, N = 0.5, colors = col)

# run scudoCytoscape (with Cytoscape open)
## Not run: scudoCytoscape(res, title = "scudoCytoscape output")

Matteo-Ciciani/scudo documentation built on Feb. 3, 2024, 9:41 a.m.