Get nodes and edges from igraph data.frame for visNetwork

Convert igraph data.frame to dataframe of nodes and edges (used as input to visNetwork). Only applicable for undirected networks.

getNodesEdges(df.data)

Arguments

df.data

igraph data.frame (output from scMiko::wgcna2graphDF)

Value

named list of nodes and edges, where each entry is a data.frame.

Examples

# get connectivity for specified module
module.name <- names(module.list.all)[names(module.list.all) %in% which.modules]
#> Error in eval(expr, envir, enclos): object 'module.list.all' not found
module.gene.cur <- module.list.all[[module.name]]
#> Error in eval(expr, envir, enclos): object 'module.list.all' not found
w.cur <- w.mat[rownames(w.mat) %in% module.gene.cur, colnames(w.mat) %in% module.gene.cur]
#> Error in eval(expr, envir, enclos): object 'w.mat' not found

# get igraph data.frame for subset of connections
w.df.top <- wgcna2graphDF(w.cur, top.n = top.n.interactions)
#> Error in igraph::graph_from_adjacency_matrix(w.mat, mode = c(graph.type),     diag = F, weighted = T): object 'w.cur' not found
w.df.top$module.membership <- module.name
#> Error in eval(expr, envir, enclos): object 'module.name' not found

# get nodes and edges
node.edge.output <- getNodesEdges(w.df.top)
#> Error in as.data.frame(d): object 'w.df.top' not found
vis.nodes <- node.edge.output$nodes
#> Error in eval(expr, envir, enclos): object 'node.edge.output' not found
vis.links <- node.edge.output$edges
#> Error in eval(expr, envir, enclos): object 'node.edge.output' not found