addClusterLabels: Label Clusters in a Network Graph Plot

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

Label Clusters in a Network Graph Plot

Description

Functions for labeling the clusters in network graph plots with their cluster IDs. The user can specify a cluster-level property by which to rank the clusters, labeling only those clusters above a specified rank.

Usage

labelClusters(
  net,
  plots = NULL,
  top_n_clusters = 20,
  cluster_id_col = "cluster_id",
  criterion = "node_count",
  size = 5, color = "black",
  greatest_values = TRUE
)

addClusterLabels(
  plot,
  net,
  top_n_clusters = 20,
  cluster_id_col = "cluster_id",
  criterion = "node_count",
  size = 5,
  color = "black",
  greatest_values = TRUE
)

Arguments

net	A list of network objects conforming to the output of buildRepSeqNetwork() or generateNetworkObjects(). See details.
plots	Specifies which plots in net$plots to annotate. Accepts a character vector of element names or a numeric vector of element position indices. The default NULL annotates all plots.
plot	A ggraph object containing the network graph plot.
top_n_clusters	A positive integer specifying the number of clusters to label. Those with the highest rank according to the criterion argument will be labeled.
cluster_id_col	Specifies the column of net$node_data containing the variable for cluster membership. Accepts a character string containing the column name.
criterion	Can be used to specify a cluster-level network property by which to rank the clusters. Non-default values are ignored unless net$cluster_data exists and corresponds to the cluster membership variable specified by cluster_id_col. Accepts a character string containing a column name of net$cluster_data. The property must be quantitative for the ranking to be meaningful. By default, clusters are ranked by node count, which is computed based on the cluster membership values if necessary.
size	The font size of the cluster ID labels. Passed to the size argument of geom_node_text().
color	The color of the cluster ID labels. Passed to the color argument of geom_node_text().
greatest_values	Logical. Controls whether clusters are ranked according to the greatest or least values of the property specified by the criterion argument. If TRUE, clusters with greater values will be ranked above those with lower values, thereby receiving a higher priority to be labeled.

Details

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

labelClusters() returns a copy of net with the specified plots annotated.

addClusterLabels() returns an annotated copy of plot.

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

addClusterMembership(), getClusterStats(), generateNetworkGraphPlots()

Examples

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

network <- buildRepSeqNetwork(
  toy_data, "CloneSeq",
  cluster_stats = TRUE,
  color_nodes_by = "cluster_id",
  color_scheme = "turbo",
  color_legend = FALSE,
  plot_title = NULL,
  plot_subtitle = NULL,
  size_nodes_by = 1
)

network <- labelClusters(network)

network$plots$cluster_id

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