R/AntibodyForests_metrics.R
AntibodyForests_metrics.RdCalculates several node metrics for the resulting AntibodyForests networks, adding these as a per-node dataframe in the new metrics slot. Must be called before AntibodyForests_plot_metrics.
AntibodyForests_metrics(
trees,
metrics,
graph.type,
features,
exclude.intermediates,
exclude.germline,
separate.bipartite,
parallel
)nested list of AntibodyForests objects or single object, as obtained from the AntibodyForests function.
vector of strings - node metric to be calculated. Currently supported metrics include: 1. Betweenness centrality - 'betweenness' 2. Closeness centrality - 'closeness' 3. Eigenvector centrality - 'eigenvector' 4. Authority score - 'authority' 5. Local and average clustering coefficients - 'local_cluster_coefficient', 'average_cluster_coefficient' 6. Strength or weighted vertex degree - 'strength' 7. Degree - 'degree' 8. Daughter nodes for directed graphs - 'daughters' 9. Vertex eccentricity (shortest path distance from the farthest other node in the graph) - 'eccentricity' 10. Pagerank algorithm values - 'pagerank' 11. Shortest (weighted) paths from germline - 'path_from_germline', 'weighted_path_from_germline' 12. Shortest(weighted) paths from the most expanded node - 'path_from_most_expanded', 'weighted_path_from_most_expanded', 13. Shortest(weighted) paths from the hub node (highest degree) - 'path_from_hub', 'weighted_path_from_hub'
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.
vector of strings - features to be considered when calculating whole-graph metrics (e.g., dominant/most abundant feature per graph).
boolean - if T, will not calculate the node-level metrics for the intermediate nodes obtained from AntibodyForests_expand_intermediates().
boolean - if T, will exclude the germline nodes from the node metric calculations.
boolean - if T and graph.type = 'heterogeneous', will separate the cell and sequence graph and calculate the node metrics independently, then recombine them in the same final graph.
boolean - whether to execute the main subroutine in parallel or not. Requires the 'parallel' R package to be installed.
nested list of AntibodyForests objects or single AntibodyForests object, with a new class slot added (metrics) = a per-node dataframe of metric values.
if (FALSE) {
AntibodyForests_metrics(trees, graph.type = 'tree', metrics = c('degree', 'pagerank'))
}