Propagate label annotations/values on sparsely labeled networks as AntibodyForests objects.

Performs label diffusion/propagation, using two different algorithms: if propagation.algorithm = 'diffusion', will perform label propagation using the graph heat diffusion method (http://mlg.eng.cam.ac.uk/zoubin/papers/CMU-CALD-02-107.pdf), 'neighbours' for neihbour majority voting propagation (https://arxiv.org/abs/0709.2938).

AntibodyForests_label_propagation(
  trees,
  features,
  propagation.algorithm,
  diffusion.n.iter,
  diffusion.threshold,
  parallel
)

Arguments

trees

nested list of AntibodyForests objects or single object, as obtained from the AntibodyForests function.

features

vector of strings - features to be propagated in the graph. Must be performed on sparsely-labeled graphs (with NA node attribute values).

propagation.algorithm

string - label propagation/diffusion algorithm to be used. If propagation.algorithm = 'diffusion', will perform label propagation using the graph heat diffusion method (http://mlg.eng.cam.ac.uk/zoubin/papers/CMU-CALD-02-107.pdf), 'neighbours' for neihbour majority voting propagation (https://arxiv.org/abs/0709.2938).

diffusion.n.iter

integer - number of diffusion iteration if propagation.algorithm = 'diffusion'.

diffusion.threshold

numeric - probability min. threshold for the diffusion algorithm.

parallel

boolean - whether to execute the main subroutine in parallel or not. Requires the 'parallel' R package to be installed.

Value

Nested list of AntibodyForests objects or single object with new propagated labels added as vertex attributes (e.g., feature_label_propagation will be a new vertex attribute in the resulting AntibodyForests objects).

Examples

if (FALSE) {
AntibodyForests_label_propagation(ova_trees,
features = 'OVA_binder',
propagation.algorithm = 'diffusion', parallel = T)
}