Calculates various tree statistics (total tree length, within-species diversity, diversity, monophyleticity and subtree length of each species) for all modules/jackknifed module versions based on a list of tree representations.
Arguments
- tree_list
A named list of
phyloobjects containing the tree representations of all modules/jackknifed module versions, with the tips of the trees corresponding to replicates. All trees are expected to have a componentspeciesthat specifies which species each tip belongs to. The trees can also contain a componentinfothat stores metadata of the module/jackknifed module version in a data frame format.- n_cores
Integer, the number of cores (default: 1).
Value
A data frame of tree statistics with the following columns:
- regulator
Character, transcriptional regulator.
- module_size
Module size, the number of target genes assigned to a regulator (only present if the column is also present in the component
infoof the trees).- type
Character, module type (orig = original or jk = jackknifed, only present if the input trees were reconstructed with jackknifing).
- id
Character, the unique ID of the module version (format: nameOfRegulator_jk_nameOfGeneRemoved in case of module type 'jk' and nameOfRegulator_orig in case of module type 'orig', only present if the input trees were reconstructed with jackknifing).
- gene_removed
Character, the name of the gene removed by jackknifing (NA in case of module type 'orig', only present if the input trees were reconstructed with jackknifing).
- within_species_diversity
Numeric, the sum of the species-wise diversities.
- total_tree_length
Numeric, the total length of all branches in the tree.
- {{species}}_diversity
Numeric, as many columns as there are species, each of them containing the the total length of the branches connecting the replicates of the given species.
- {{species}}_monophyl
Logical, as many columns as there are species, each of them indicating whether the tree is monophyletic for the replicates of the given species.
- {{species}}_subtree_length
Numeric, as many columns as there are species, each of them containing the sum of the branch lengths in the subtree that is defined by the replicates of the species and includes the internal branch connecting these replicates to the rest of the tree. NA if the tree is not monophyletic for the replicates of the given species.
Details
As part of the CroCoNet approach, pairwise module preservation scores are calculated between replicates, both within and across species (see calculatePresStats) and neighbor-joining trees are reconstructed based on these preservation scores per module (see convertPresToDist and reconstructTrees). The tips of the resulting tree represent the replicates and the branch lengths represent the dissimilarity of module connectivity patterns between the networks of 2 replicates.
Various useful statistics can be defined based on these module trees:
Total tree length: The sum of all branch lengths in the tree; measures module variability both within and across species.
Diversity of a species: The total length of the branches connecting the replicates of the given species to each other; measures module variability within this particular species.
Within-species diversity: The sum of the diversity values across all species; measures module variability within species in general.
Monophyleticity of a species: Indicates whether the tree is monophyletic for the replicates of the given species. Only if a module tree is monophyletic for a species of interest can the module be tested for divergence between this species and all others.
Subtree length of a species: The sum of the branch lengths in the subtree that is defined by the replicates of the species and includes the internal branch connecting these replicates to the rest of the tree. Undefined if the tree is not monophyletic for the species of interest.
In the later steps of the pipeline, these tree-based statistics can be used to 1) identify modules that are conserved, diverged overall or diverged between a species and all others (see findConservedDivergedModules), and 2) pinpoint individual target genes within these modules that contribute the most to the conservation/divergence (see findConservedDivergedTargets).