Update module names in an existing graph object

Usage

update_graph_modules(
  graph_obj,
  modules,
  old_col = NULL,
  new_col = NULL,
  levels = NULL,
  allow_partial = TRUE
)

Arguments

graph_obj: A graph object returned by build_graph_*().
modules: A named vector or a data frame used to rename modules. The mapping is old_module -> new_module.
old_col: Character. Old-module column name in modules when modules is a data frame. Default NULL means auto-detect.
new_col: Character. New-module column name in modules when modules is a data frame. Default NULL means auto-detect.
levels: Character vector. Optional explicit module order. If NULL, order by module size (descending) and place "Others" at the end.
allow_partial: Logical (default = TRUE). If TRUE, modules without rename rules keep original names. If FALSE, all existing modules must be covered by modules.

Value

A new graph object with updated module-related node attributes: Modularity, modularity2, and modularity3 (and modularity if that column exists).

Examples

data(ppi_example)
obj <- build_graph_from_df(
  df              = ppi_example$ppi,
  node_annotation = ppi_example$annotation
)
obj2 <- update_graph_modules(
  graph_obj = obj,
  modules   = c("1" = "ModuleA", "2" = "ModuleB")
)
levels(get_graph_nodes(obj2)$Modularity)
#>  [1] "10"      "11"      "12"      "13"      "14"      "15"      "16"     
#>  [8] "17"      "18"      "19"      "20"      "21"      "22"      "ModuleA"
#> [15] "ModuleB" "Others"