Correspondence between the module ID (msp or functional module) and its name (bacteria or function)

Usage

module_to_node(
  module,
  annotation_table,
  col_module_id = "msp_name",
  annotation_level
)

Arguments

module: String. The name of the biological object (msp or functional module), can be a single one or a list
annotation_table: Dataframe. The dataframe gathering the taxonomic or functional module correspondence information
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

Value

Dictionary. The name of the module, can be a single one or a list

Examples

df_taxo <- data.frame(
  msp_name = c("msp_1", "msp_2", "msp_3", "msp_4"),
  genus = c("A", "B", "C", "D"),
  species = c("A a", "B a", "C c", "D b")
)
# Correspondence for one specific msp
module_to_node("msp_1", annotation_table = df_taxo, col_module_id = "msp_name", annotation_level = "species")
#> [1] "A a"
# or for several msps
module_to_node(c("msp_1", "msp_3", "msp_4"), annotation_table = df_taxo, col_module_id = "msp_name", annotation_level = "species")
#> [1] "A a" "C c" "D b"
# and if one msp is repeated
module_to_node(c("msp_1", "msp_1", "msp_2"), annotation_table = df_taxo, col_module_id = "msp_name", annotation_level = "genus")
#> [1] "A" "A" "B"