Display network after applying NeighborFinder

Usage

visualize_network(
  res_NeighborFinder,
  annotation_table,
  col_module_id,
  annotation_level,
  object_of_interest,
  annotation_option = FALSE,
  node_size = 12,
  label_size = 4,
  object_color = "cadetblue2",
  seed = NULL
)

Arguments

res_NeighborFinder: Dataframe. The result from apply_NeighborFinder()
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 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
annotation_option: Boolean. Default value is False. If True: labels on nodes become module names instead of module IDs
node_size: Numeric. The parameter to adjust size of nodes
label_size: Numeric. The parameter to adjust size of labels
object_color: String. The name of the color to differentiate the nodes corresponding to 'object_of_interest' from the other module IDs
seed: Numeric. The seed number, ensuring reproducibility

Value

Network. Visualization of NeighborFinder results. Edge color encodes coefficient sign: green if positive, red if negative; edge width encodes magnitude.

Examples

data(taxo)
visualize_network(
  result_example$res_CRC_JPN,
  taxo,
  object_of_interest = "Escherichia coli",
  col_module_id = "msp_id",
  annotation_level = "species",
  label_size = 5
)

# #With species names instead of msp names
# visualize_network(
#   result_example$res_CRC_JPN,
#   taxo,
#   object_of_interest = "Escherichia coli",
#   col_module_id = "msp_id",
#   annotation_level = "species",
#   label_size = 5,
#   annotation_option = TRUE,
#   seed = 2
# )
# #With esthetic changes
# visualize_network(
#   result_example$res_CRC_JPN,
#   taxo,
#   object_of_interest = "Escherichia coli",
#   col_module_id = "msp_id",
#   annotation_level = "species",
#   annotation_option = TRUE,
#   node_size = 15,
#   label_size = 6,
#   object_color = "orange",
#   seed = 2
# )