scudoCytoscape: Create a Cytoscape network from the output of scudoNetwork

Description Usage Arguments Value Author(s) See Also Examples

View source: R/scudoCytoscape.R

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

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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 matteo.ciciani@gmail.com, Thomas Cantore cantorethomas@gmail.com

See Also

scudoNetwork, RCy3

Examples

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# 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 May 24, 2020, 5:34 a.m.