Create a cnetplot igraph object

Source: R/jamenrich-igraph.r

Create a cnetplot igraph object

cnetplotJam(
  x,
  showCategory = 5,
  categorySize = "geneNum",
  nodeLabel = c("Name", "Description", "ID"),
  foldChange = NULL,
  fixed = TRUE,
  doPlot = FALSE,
  categoryColor = "#E5C494",
  geneColor = "#B3B3B3",
  normalizeGeneSize = TRUE,
  labelCex = 0.45,
  colorSub = NULL,
  verbose = FALSE,
  ...
)

Arguments

x

enrichResults object

showCategory

integer number of categories to include in the resulting Cnet plot.

categorySize

character value indicating how to size the pathway nodes, where "geneNum" sizes nodes by the number of genes in that pathway, and "pvalue" sizes nodes by the enrichment P-value using the format -log10(pvalue).

nodeLabel

character value indicating which colname in as.data.frame(x) to use as a node label. Depending upon the source of data, there may be alternative colnames that are more suitable as node labels.

foldChange

numeric vector named by gene, or NULL. When supplied, the vector names must use the same nomenclature as the x input object, which can be inspected with print(head(x@gene)).

fixed

optional argument passed to netplot.

doPlot

logical indicating whether to plot the result.

categoryColor, geneColor

character color, used to colorize category (pathway) nodes, or gene nodes, respectively.

normalizeGeneSize

logical indicating whether to re-scale the gene node sizes so the mean gene node size is no larger than the median category node size. This option is intended to help gene and category node sizes to be in relative proportion.

labelCex

numeric value to re-scale label text in the igraph object, and is applied directly to the igraph object.

colorSub

character vector of valid R colors, whose names are compared to node names, for example V(g)$name %in% names(colorSub).

verbose

logical indicating whether to print verbose output.

...

additional arguments are ignored.

Details

The purpose of this function is to mimic the steps in DOSE:::cnetplot() except not plot the output, and provide some customizations.

This function calls cnetplot_internalJam(), which among other things adds a node attribute to the resulting igraph, "nodeType", where nodeType="Gene" identifies gene nodes, and nodeType="Set" identifies pathway/gene set nodes.