Plot gene coexpression network from edge list

Usage

plot_gcn(
  edgelist_gcn,
  net,
  color_by = "module",
  hubs = NULL,
  show_labels = "tophubs",
  top_n_hubs = 5,
  curvature = 0,
  interactive = FALSE,
  dim_interactive = c(600, 600)
)

Arguments

edgelist_gcn: Data frame containing the edge list for the GCN. The edge list can be generated with get_edge_list().
net: List object returned by exp2net.
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 show_labels equals "tophubs". Default is 5.
curvature: Numeric indicating the amount of curvature in edges. Negative values produce left-hand curves, positive values produce right-hand curves, and zero produces a straight line. Default: 0.1.
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).

Value

A ggplot object.

Author

Fabricio Almeida-Silva

Examples

data(filt.se)
gcn <- exp2gcn(filt.se, SFTpower = 18, cor_method = "pearson")
#> ..connectivity..
#> ..matrix multiplication (system BLAS)..
#> ..normalization..
#> ..done.
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)