scudoCytoscape {rScudo} | R Documentation |
A wrapper to RCy3
function calls to plot the result of
scudoNetwork
in Cytoscape 3. Cytoscape must be open before
running this function.
scudoCytoscape(graph, title = "Scudo Graph", collection = "SCUDO")
graph |
object of class |
title |
the title of the network |
collection |
the name of the Cytoscape collection |
The network SUID (an integer).
Matteo Ciciani matteo.ciciani@gmail.com, Thomas Cantore cantorethomas@gmail.com
# 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")