plot_rwr_subnetwork: Plot RWR subnetwork

In abodein/netOmics: Multi-Omics (time-course) network-based integration and interpretation

Plot RWR subnetwork

Description

Display the subgraph from a RWR results. This function colors adds a specific color to each node based on their 'type' attribute. It also adds a legend including the number of vertices/edges and the number of nodes of specific type. Additionally, the function can display any igraph object.

Usage

plot_rwr_subnetwork(X, color = NULL, plot = TRUE, legend = TRUE, ...)

Arguments

X	an igraph object
color	(optional) a named character vector or list, list of color to apply to each type
plot	logical, if TRUE then the plot is produced
legend	(optional) logical, if TRUE then the legend is displayed with number of veretices/edges and the number of nodes of specific type.
...	Arguments to be passed to the plot method

Value

X is returned with additional vertex attributes

Examples

graph1 <- igraph::graph_from_data_frame(
    list(from = c("A", "B", "A", "D", "C", "A", "C"), 
         to = c("B", "C", "D", "E", "D", "F", "G")), 
    directed = FALSE)
graph1 <- igraph::set_vertex_attr(graph = graph1,
                                  name = 'type', 
                                  index = c("A","B","C"),
                                  value = "1")
graph1 <- igraph::set_vertex_attr(graph = graph1, 
                                  name = 'type', 
                                  index = c("D","E"),
                                  value = "2")
graph1 <- igraph::set_vertex_attr(graph = graph1, 
                                  name = 'type', 
                                  index = c("F", "G"),
                                  value = "3")

rwr_res <- random_walk_restart(X = graph1, 
                               seed = c("A"))
rwr_res_type <- rwr_find_seeds_between_attributes(X = rwr_res, 
                                                  attribute = "type")

plot_rwr_subnetwork(rwr_res_type$A)

abodein/netOmics documentation built on Oct. 20, 2024, 9:25 a.m.