addNodeStats: Compute Node-Level Network Properties

In mlizhangx/Network-Analysis-for-Repertoire-Sequencing-: Network Analysis of Immune Repertoire

Compute Node-Level Network Properties

Description

Given a list of network objects returned by buildRepSeqNetwork() or generateNetworkObjects(), computes a specified set of network properties for the network nodes. The list of network objects is returned with each property added as a variable to the node metadata.

Usage

addNodeStats(
  net,
  stats_to_include = chooseNodeStats(),
  cluster_fun = "fast_greedy",
  cluster_id_name = "cluster_id",
  overwrite = FALSE,
  verbose = FALSE,
  ...
)

Arguments

net	A list of network objects conforming to the output of buildRepSeqNetwork() or generateNetworkObjects(). See details.
stats_to_include	Specifies which network properties to compute. Accepts a vector created using chooseNodeStats() or exclusiveNodeStats(), or the character string "all" to compute all network properties.
cluster_fun	A character string specifying the clustering algorithm to use when computing cluster membership. Applicable only when stats_to_include = "all" or stats_to_include["cluster_id"] is TRUE. Passed to addClusterMembership().
cluster_id_name	A character string specifying the name of the cluster membership variable to be added to the node metadata. Applicable only when stats_to_include = "all" or stats_to_include["cluster_id"] is TRUE. Passed to addClusterMembership().
overwrite	Logical. If TRUE and net$node_data contains a variable whose name matches the value of cluster_id_name, then its values will be overwritten with new cluster membership values (obtained using addClusterMembership(), to which the values of cluster_fun, overwrite). Applicable only when stats_to_include = "all" or stats_to_include["cluster_id"] is TRUE.
verbose	Logical. If TRUE, generates messages about the tasks performed and their progress, as well as relevant properties of intermediate outputs. Messages are sent to stderr().
...	Named optional arguments to the function specified by cluster_fun.

Details

Node-level network properties are properties that pertain to each individual node in the network graph.

Some are local properties, meaning that their value for a given node depends only on a subset of the nodes in the network. One example is the network degree of a given node, which represents the number of other nodes that are directly joined to the given node by an edge connection.

Other properties are global properties, meaning that their value for a given node depends on all of the nodes in the network. An example is the authority score of a node, which is computed using the entire graph adjacency matrix (if we denote this matrix by A, then the principal eigenvector of A^T A represents the authority scores of the network nodes).

See chooseNodeStats() for a list of the available node-level network properties.

The list net must contain the named elements igraph (of class igraph), adjacency_matrix (a matrix or dgCMatrix encoding edge connections), and node_data (a data.frame containing node metadata), all corresponding to the same network. The lists returned by buildRepSeqNetwork() and generateNetworkObjects() are examples of valid inputs for the net argument.

Value

A modified copy of net, with net$node_data containing an additional column for each new network property computed. See chooseNodeStats() for the network property names, which are used as the column names, except for the cluster membership variable, whose name is the value of cluster_id_name.

Author(s)

Brian Neal ([e-mail])

References

Hai Yang, Jason Cham, Brian Neal, Zenghua Fan, Tao He and Li Zhang. (2023). NAIR: Network Analysis of Immune Repertoire. Frontiers in Immunology, vol. 14. doi: 10.3389/fimmu.2023.1181825

Webpage for the NAIR package

See Also

chooseNodeStats()

Examples

set.seed(42)
toy_data <- simulateToyData()

net <- generateNetworkObjects(
  toy_data, "CloneSeq"
)

# Add default set of node properties
net <- addNodeStats(net)

# Modify default set of node properties
net <- addNodeStats(
  net,
  stats_to_include =
    chooseNodeStats(
      closeness = TRUE,
      page_rank = FALSE
    )
)

# Add only the spepcified node properties
net <- addNodeStats(
  net,
  stats_to_include =
    exclusiveNodeStats(
      degree = TRUE,
      transitivity = TRUE
    )
)

# Add all node-level network properties
net <- addNodeStats(
  net,
  stats_to_include = "all"
)

mlizhangx/Network-Analysis-for-Repertoire-Sequencing- documentation built on April 7, 2024, 12:02 p.m.