Display the intersection network from 2 or more datasets

Usage

intersections_network(
  res_list,
  threshold,
  annotation_table,
  col_module_id,
  annotation_level,
  object_of_interest,
  annotation_option = FALSE,
  node_size = 12,
  label_size = 4,
  edge_label_size = 2,
  object_color = "cadetblue2",
  seed = NULL
)

Arguments

res_list: List of dataframes. The results from apply_NeighborFinder() on several datasets
threshold: Numeric. Integer corresponding to the minimum number of datasets in which you want neighbors to have been found
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
edge_label_size: Numeric. The parameter to adjust the size of edge 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 from several datasets

Examples

data(taxo)
data(data)
data(metadata)
res_CRC_JPN <- apply_NeighborFinder(data$CRC_JPN, object_of_interest = "Escherichia coli", col_module_id = "msp_id", annotation_level = "species")
res_CRC_CHN <- apply_NeighborFinder(data$CRC_CHN, object_of_interest = "Escherichia coli", col_module_id = "msp_id", annotation_level = "species", covar = ~study_accession, meta_df = metadata$CRC_CHN, sample_col = "secondary_sample_accession")
res_CRC_EUR <- apply_NeighborFinder(data$CRC_EUR, object_of_interest = "Escherichia coli", col_module_id = "msp_id", annotation_level = "species", covar = ~study_accession, meta_df = metadata$CRC_EUR, sample_col = "secondary_sample_accession")

intersections_network(res_list = list(res_CRC_JPN, res_CRC_CHN, res_CRC_EUR), taxo, threshold = 2, "Escherichia coli", col_module_id = "msp_id", annotation_level = "species", label_size = 7, edge_label_size = 4, node_size = 15, annotation_option = TRUE, seed = 3)