GenerateNetwork: Generate a gene-network to perform a KEGG pathway analysis on...
In cosmonet-package/COSMONET: Screening-network Cox methods for survival analysis

This function creates an interactive dashboard with two tabs. The first tab "Not-Isolated Genes" shows a three-colour networks of the not-isolated genes, i.e. the genes sharing at least one KEGG pathway. The second tab "Full Network" shows a three-colour networks of all the genes selected by the method (all the not zero signatures). Different node colors are used to show a probability measure between the genes and the disease under investigation as follows: Blue color is used for the bottom 501 tissue-specific genes (mapped down genes), White color is used for genes that are not listed as tissue-specific in the HumanBase database (not mapped genes).

GenerateNetwork(
  ListOfGenes = NULL,
  header = TRUE,
  diseaseID = NULL,
  nodesCols = c("#EFCFD4", "#D9E3FC", "#FFFFFF")
)

`ListOfGenes`	a two-column data frame composed by gene names and beta coefficients
`diseaseID`	the disease ID identified by Disease Ontology (DO) (https://disease-ontology.org)
`ListHeader`	true if the genes' list has a header, false otherwise
`nodesCol`	the colours of the nodes. Default values are orange, greeen and purple for mapped-up, mapped down and not mapped genes, respectively.