# Networks

Networks can be displayed to represent the relevant associations between X and Y variables, they are inferred using a pairwise association score between X and Y variables. The user can set a threshold to represent only the variables X and Y with an association score greater than the threshold. By changing this threshold, the user can choose to include or exclude relationships in the relevance network. The output is a graph where each X- and Y-variable corresponds to a node and the edges included in the graph portray associations between them.

# Usage in mixOmics

Networks graphs can be obtained in mixOmics via the function network as displayed below:

library(mixOmics)

## Will work with sPLS result
data(liver.toxicity)

X <- liver.toxicity$gene Y <- liver.toxicity$clinic
toxicity.spls <- spls(X, Y, ncomp = 3)

network(toxicity.spls,
color.node = c("orange","blue"),
threshold = 0.75,
row.names = FALSE,
col.names = FALSE)

network(toxicity.spls,color.edge = c("red","orange","cyan","blue"),row.names=FALSE, threshold = 0.75)

 network(toxicity.spls,lty.edge='dotted',row.names = FALSE, threshold = 0.75)


We can export the graph to Cytoscape file format using write.graph from the igraph package.

net.result <- network(toxicity.spls)

write.graph(net.result\$gR, file = "network.gml", format = "gml")


# References

González I., Lê Cao K.-A., Davis, M.D. and Déjean S. (2013) Insightful graphical outputs to explore relationships between two ‘omics’ data sets. BioData Mining 5:19