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Plot a Local Network Around a Target Node from tKOI Results

plot_network.Rd

This function visualizes a subnetwork of biologically relevant nodes around a specified target node from a tKOI result. It includes all significant genes (based on p-value and logFC thresholds) within a user-defined network neighborhood, as well as all connecting paths between the target and these genes. The resulting network is colored by log fold change (logFC), sized by beta value, and plotted with an igraph layout.

Usage

plot_network(
  tkoi_result,
  target_node_id,
  degree_expansion = 2,
  network_layout_type = "kk"
)

Arguments

tkoi_result

An object of class tkoi_result containing differential expression results, thresholds, and network information from a tKOI analysis.

target_node_id

A character string specifying the node ID (e.g., GO term) to center the network around.

degree_expansion

Integer specifying the maximum graph distance from the target node to explore. Defaults to 2.

network_layout_type

A character string indicating the layout algorithm to use for plotting. Options include: "kk" (Kamada-Kawai), "fr" (Fruchterman-Reingold), "gem" (Graph Embedding), "graphopt" (Graph Optimization), "lgl" (Large Graph Layout), and "mds" (Multidimensional Scaling).

Value

A network plot is rendered directly using plot.igraph().

Details

The function first identifies differentially expressed genes that meet user-defined thresholds and are within the specified graph neighborhood of the target node. It then computes all simple paths between the target node and each significant gene, compiles a list of nodes involved, and builds a subgraph.

Each node is colored by logFC (gradient), or gray if not a gene. The target node is highlighted in orange. Node sizes are scaled to beta values. The layout algorithm used can be selected with network_layout_type.

Examples

if (FALSE) { # \dontrun{
plot_network(tkoi_result = my_tkoi_result,
             target_node_id = "4:c77f6410-bc08-43ba-a172-0503ab1c93db:1234567",
             degree_expansion = 2,
             network_layout_type = "kk")
} # }