igraph enrichment map to ggraph plot — plot_enrichment_map

Takes in the output from enrichment_map_oae() or enrichment_map_gsea() and generates a ggraph object for subsequent saving, etc.

Usage

plot_enrichment_map_ggraph(
  g,
  label_nodes = "adaptive",
  labels_to_include = NULL,
  adaptive_thresholds = c(`15` = 3, `5` = 2, `2` = 1, `1` = 0),
  font_size = 4,
  ...
)

Arguments

g

igraph. Output from enrichment_map functions.

label_nodes

String. Controls which nodes to label. Options:

"all": Label all nodes
"adaptive": Adaptive labelling based on community size (default)
NULL: No labels
Integer: Label top N nodes by size

labels_to_include

Optional string. These are labels you want to include no matter what.

adaptive_thresholds

Named numeric. The names indicate the community size and the values how many pathways per community to show. An example would be c("15" = 3, "5" = 2, "2" = 1, "1" = 0), which is also the default.

font_size

Numeric. Font size of the labels on top of the enrichment map.

...

Other parameters you wish to forward to ggraph::geom_node_text().

Value

A ggplot2 object with the enrichment map