Title Query and plot the sub-graph

Title Query and plot the sub-graph

visNet(
  ig,
  metabolite_query = NULL,
  gene_query = NULL,
  metabolite_by = c("symbol", "refmet_name", "HMDB_ID", "name"),
  gene_by = c("symbol", "ensemble_ID", "name"),
  focus = c("all", "metabolite", "pathway"),
  edge_label = NULL,
  main = "A simple reaction-based network",
  metabolite_query_color = "#FF9999",
  gene_query_color = "#56B4E9",
  associated_metabolite_color = "#808080",
  associated_gene_color = "#808080",
  metabolite_shape = "dot",
  gene_shape = "diamond",
  hover = TRUE,
  stabilization = FALSE,
  igraph_layout = "layout_with_fr",
  layout_seed = 42
)

Arguments

ig

the igraph object derived from a given GEM

metabolite_query

a character vector contains metabolites which are consistent with V(ig)$symbol or V(ig)$name, for metabolite, the "symbol" should be consistent with "fullname" column in hypeR_GEM_obj$mapped_metabolite_signatures

gene_query

a character vector contains enzyme-coding genes which are consistent with V(ig)$symbol or V(ig)$name

metabolite_by

type of symbols used by metabolite_query

gene_by

type of symbols used by gene_query

focus

focus of the subgraph query

edge_label

An edge attribute in E(ig) that can be used to represent edge labels

main

the title of the network

metabolite_query_color

the node color of "metabolite_query"

gene_query_color

the node color of "gene_query"

associated_metabolite_color

the node color of metabolites other than "metabolite_query"

associated_gene_color

the node color of genes other than "gene_query"

metabolite_shape

the node shape of metabolites

gene_shape

the node shape of genes

hover

logical variable

stabilization

logical variable

igraph_layout

the layout algorithm available in "igraph", see https://igraph.org/r/html/1.3.0/layout_.html

layout_seed

random seed of the network layout

Value

a list of: ig = node-induced sub-graph, p = a visNetwork object