Calculates the node transitions frequencies for a given feature and an AntibodyForests object — AntibodyForests_node

Node transitions represent the number of (un)directed edges between two feature values of a given feature type in a single sequence similarity network or minimum spanning trees (e.g., between VDJ_cgene = 'IGHA' and VDJ_cgene = 'IGHM'). The resulting AntibodyForests objects will contain a new slot - node_transitions. Will also output bar plots of the transition frequencies.

AntibodyForests_node_transitions(
  trees,
  features,
  combined,
  graph.type,
  permutation.test,
  exclude.germline,
  exclude.intermediates,
  n.permutations,
  plot.results,
  parallel
)

Arguments

trees: nested list of AntibodyForests objects or single object, as obtained from the AntibodyForests function.
features: vector of strings - features for the node transition counting. Each node will be assigned the dominant feature if its constituent cells have different feature values (e.g., for features = c('seurat_clusters')). These features need to be first added as vertex attributes when creating the AntibodyForests networks, specified in the node.features parameter of AntibodyForests.
combined: boolean - if T, will assign a new feature by combining the feature values as specified in the features parameter (e.g., if node 1 has VDJ_cgene = 'IGHM' and seurat_clusters = 1, will create a new feature = 'IGHM 1' for that node, for joint node transitions).
graph.type: string - the graph type available in the AntibodyForests object which will be used as the function input. Currently supported network/analysis types: 'tree' (for the minimum spanning trees or sequence similarity networks obtained from the main AntibodyForests function), 'heterogeneous' for the bipartite graphs obtained via AntibodyForests_heterogeneous, 'dynamic' for the dynamic networks obtained from AntibodyForests_dynamics.
permutation.test: boolean - if T, will perform a permutation statistical test on the node feature transition values.
exclude.germline: boolean - if T, will exclude the germline from the node feature transitions counting.
exclude.intermediates: boolean - if T, will exclude the intermediate nodes expanded using AntibodyForests_expand_intermediates() from the node transitions counting.
n.permutations: integer - number of node feature permutations for the permutation test.
plot.results: boolean - if T, will display the node transitions counts as bar plots, per feature specified in the features parameter.
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 for each clonotype and each sample or single object, with an additional node_transitions slot of transition/edge counts.

Examples

if (FALSE) {
AntibodyForests_node_transitions(trees,
graph.type = 'tree', features = 'VDJ_cgene',
plot.results = T)
}