Extract edges in graph involving any module in object_of_interest set

Usage

prev_for_selected_nodes(
  data_with_annotation,
  graph_file,
  col_module_id,
  annotation_level,
  object_of_interest = NULL
)

Arguments

data_with_annotation: Dataframe. The abundance table merged with the module names. Required format: modules are the rows and samples are the columns. The first column must be the modules name (e.g. species), the second is the module ID (e.g. msp), and each subsequent column is a sample
graph_file: Dataframe. The object generated by graph_step() function
col_module_id: String. The name of the column with the module names in annotation_table
annotation_level: String. The name of the column with the level to be studied. Examples: species, genus, level_1
object_of_interest: String. The name of the bacteria or species of interest or a key word in the functional module definition

Value

Dataframe. The dataframe of edges in the graph involving modules corresponding to object_of_interest and their corresponding prevalences.

Examples

tiny_data <- data.frame(
  species = c("One bacteria", "One bacterium L", "One bacterium G", "Two bact"),
  msp_name = c("msp_1", "msp_2", "msp_3", "msp_4"),
  SAMPLE1 = c(0, 1.328425e-06, 0, 1.527688e-07),
  SAMPLE2 = c(1.251707e-07, 1.251707e-07, 3.985320e-07, 0),
  SAMPLE3 = c(0, 0, 4.926046e-09, 5.626392e-06),
  SAMPLE4 = c(0, 0, 2.98320e-05, 0)
)
tiny_graph <- graph_step(tiny_data, col_module_id = "msp_name", annotation_level = "species", seed = 20242025) %>% suppressWarnings()

tiny_truth <- prev_for_selected_nodes(tiny_data, tiny_graph, col_module_id = "msp_name", annotation_level = "species", object_of_interest = "bacterium")