Find group-specific clusters based on user-defined species classification

Usage

find_GS_clusters(
  profile_matrix = NULL,
  species_annotation = NULL,
  min_percentage = 50
)

Arguments

profile_matrix: A matrix of phylogenomic profiles obtained with phylogenomic_profile.
species_annotation: A 2-column data frame with species IDs in the first column (same as column names of profile matrix), and species annotation (e.g., higher-level taxonomic information) in the second column.
min_percentage: Numeric scalar with the minimum percentage of species in a group to consider group specificity. For instance, if a given cluster is present in only 1 group of species, but in less than min_percentage of the species for this group, it will not be considered a group-specific cluster. This filtering criterion is useful to differentiate group-specific clusters (e.g., family-specific) from subgroup-specific clusters (e.g., genus-specific). Default: 50.

Value

A data frame with the following variables:

Group: To which group of species the cluster is specific.
Percentage: Percentage of species from the group that are represented by the cluster.
Cluster: Cluster ID.

Examples

data(clusters)
profile_matrix <- phylogenomic_profile(clusters)

# Species annotation
species_order <- c(
    "vra", "van", "pvu", "gma", "cca", "tpr", "mtr", "adu", "lja",
    "Lang", "car", "pmu", "ppe", "pbr", "mdo", "roc", "fve",
    "Mnot", "Zjuj", "hlu", "jcu", "mes", "rco", "lus", "ptr"
)
species_annotation <- data.frame(
   Species = species_order,
   Family = c(rep("Fabaceae", 11), rep("Rosaceae", 6),
              "Moraceae", "Ramnaceae", "Cannabaceae",
               rep("Euphorbiaceae", 3), "Linaceae", "Salicaceae")
)
gs_clusters <- find_GS_clusters(profile_matrix, species_annotation)