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

Examples

data(taxo)
data(data)
res_CRC_JPN <- apply_NeighborFinder(data$CRC_JPN, object_of_interest = "Escherichia coli", col_module_id = "msp_id", annotation_level = "species")
visualize_network(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(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(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)