Create gene-set network plot object

Create gene-set network plot object

make_gsNetwork(
  normalisedScores,
  gsTopology,
  colorBy = c("robustZ", "pvalue"),
  foldGSname = TRUE,
  foldafter = 2
)

Arguments

normalisedScores

A dataframe as described in the details section

gsTopology

List of pathway topology matrices generated using function retrieve_topology

colorBy

Choose to color nodes either by "robustZ" or "pvalue". A column must exist in the normalisedScores for the chosen parameter

foldGSname

logical(1). Should long gene-set names be folded into two lines

foldafter

The number of words after which gene-set names should be folded. Defaulted to 2

Value

igraph object