Generate a graph with a "cluster-like" structure, only needed for simulation purposes

Usage

graph_step(
  data_with_annotation,
  col_module_id,
  annotation_level,
  seed = 10010,
  data_type = "shotgun"
)

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
col_module_id: String. The name of the column with the module names in the annotation table
annotation_level: String. The name of the column with the level to be studied. Examples: species, genus, level_1
seed: Numeric. Seed number for data generation (new_synth_data)
data_type: String. Enables the treatment of 16S data with "16S", default value is "shotgun"

Value

Dataframe. The dataframe is composed of 0 and 1 corresponding to the existence of edges on the graph.

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()