plot_gcn {BioNERO} | R Documentation |
Plot gene coexpression network from edge list
plot_gcn( edgelist_gcn, net, color_by = "module", hubs = NULL, show_labels = "tophubs", top_n_hubs = 5, interactive = FALSE, dim_interactive = c(600, 600) )
edgelist_gcn |
Data frame containing the edge list for the GCN.
The edge list can be generated with |
net |
List object returned by |
color_by |
How should nodes be colored? It must be either "module" (nodes will have the colors of their modules) or a 2-column data frame containing genes in the first column and a custom gene annotation in the second column. Default: "module". |
hubs |
Data frame containing hub genes in the first column, their modules in the second column, and intramodular connectivity in the third column. |
show_labels |
Character indicating which nodes will be labeled. One of "all", "allhubs", "tophubs", or "none". Default: tophubs. |
top_n_hubs |
Number of top hubs to be labeled. It is only valid
if |
interactive |
Logical indicating whether the network should be interactive or not. Default is FALSE. |
dim_interactive |
Numeric vector with width and height of window for interactive plotting. Default: c(600,600). |
A ggplot object.
Fabricio Almeida-Silva
simplify
,as_data_frame
,gorder
igraph_to_networkD3
,forceNetwork
geom_edges
,geom_nodes
,geom_nodetext
,theme_blank
,geom_nodetext_repel
ggplot
,aes_
data(filt.se) gcn <- exp2gcn(filt.se, SFTpower = 18, cor_method = "pearson") gcn_edges <- get_edge_list(gcn, module="brown", filter=TRUE, method="min_cor") hubs <- get_hubs_gcn(filt.se, gcn) p <- plot_gcn(gcn_edges, gcn, hubs = hubs)