Plot the Graph of an Immune Repertoire Network

Given the igraph of an immune repertoire network, generates a plot of the network graph according to the user specifications.

Deprecated. Replaced by addPlots().

Usage

plotNetworkGraph(
  igraph,
  plot_title = NULL,
  plot_subtitle = NULL,
  color_nodes_by = NULL,
  color_scheme = "default",
  color_legend = "auto",
  color_title = "auto",
  edge_width = 0.1,
  size_nodes_by = 0.5,
  node_size_limits = NULL,
  size_title = "auto",
  outfile = NULL,
  pdf_width = 12,
  pdf_height = 8
)

Arguments

igraph: An object of class igraph.
plot_title: A character string containing the plot title. Passed to labs().
plot_subtitle: A character string containing the plot subtitle. Passed to labs().
color_nodes_by: A vector whose length matches the number of nodes in the network. The values are used to encode the color of each node. An argument value of NULL (the default) leaves the nodes uncolored. Passed to the color aesthetic mapping of geom_node_point().
color_scheme: A character string specifying the color scale used to color the nodes. "default" uses default ggplot() colors. Other options are one of the viridis color scales (e.g., "plasma", "A" or other valid inputs to the option argument of scale_color_viridis()) or (for discrete variables) a palette from hcl.pals() (e.g., "RdYlGn"). Each of the viridis color scales can include the suffix "-1" to reverse its direction (e.g., "plasma-1" or "A-1").
color_legend: A logical scalar specifying whether to display the color legend in the plot. The default value of "auto" shows the color legend if color_nodes_by is a continuous variable or a discrete variable with at most 20 distinct values.
color_title: A character string (or NULL) specifying the title for the color legend. Only applicable if color_nodes_by is a vector. If color_title = "auto" (the default), the title for the color legend will be the name of the vector provided to color_nodes_by.
edge_width: A numeric scalar specifying the width of the graph edges in the plot. Passed to the width argument of geom_edge_link0().
size_nodes_by: A numeric scalar specifying the size of the nodes, or a numeric vector with positive entires that encodes the size of each node (and whose length matches the number of nodes in the network). Alternatively, an argument value of NULL uses the default ggraph() size for all nodes. Passed to the size aesthetic mapping of geom_node_point().
size_title: A character string (or NULL) specifying the title for the size legend. Only applicable if size_nodes_by is a vector. If size_title = "auto" (the default), the title for the color legend will be the name of the vector provided to size_nodes_by.
node_size_limits: A numeric vector of length 2, specifying the minimum and maximum node size. Only applicable if size_nodes_by is a vector. If node_size_limits = NULL, the default size scale will be used.
outfile: An optional file path for saving the plot as a pdf. If NULL (the default), no pdf will be saved.
pdf_width: Sets the plot width when writing to pdf. Passed to the width argument of pdf().
pdf_height: Sets the plot height when writing to pdf. Passed to the height argument of pdf().

Value

A ggraph object.

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

Network Visualization article on package website

Author

Brian Neal (Brian.Neal@ucsf.edu)

Examples

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

# Generate network for data
net <- buildNet(toy_data, "CloneSeq")

# Plot network graph
net_plot <- plotNetworkGraph(
  net$igraph,
  color_nodes_by =
    net$node_data$SampleID,
  color_title = NULL,
  size_nodes_by =
    net$node_data$CloneCount,
  size_title = "Clone Count",
  node_size_limits = c(0.5, 1.5))
#> Warning: `plotNetworkGraph()` was deprecated in NAIR 1.0.1.
#> ℹ Please use `addPlots()` instead.

print(net_plot)