Plot gene regulatory network from edge list

Usage

plot_grn(
  edgelist_grn,
  show_labels = "tophubs",
  top_n_hubs = 5,
  layout = igraph::with_kk,
  arrow.gap = 0.01,
  ranked = TRUE,
  curvature = 0.1,
  interactive = FALSE,
  dim_interactive = c(600, 600)
)

Arguments

edgelist_grn: Data frame containing the edge list for the GRN network. First column is the TF and second column is the target gene. All other columns are interpreted as edge attributes.
show_labels: Character indicating which nodes will be labeled. One of "all", "allhubs", "tophubs", or "none".
top_n_hubs: Number of top hubs to be labeled. It is only valid if show_labels equals "tophubs". Default is 5.
layout: igraph function for the network layout. One of with_dh, with_drl, with_gem, with_lgl, with_fr, with_graphopt, with_kk and with_mds. Default is with_kk.
arrow.gap: Numeric indicating the distance between nodes and arrows. Default is 0.2.
ranked: Logical indicating whether to treat third column of the edge list (edge weights) as ranked values. Default: TRUE.
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 containing the network.

Author

Fabricio Almeida-Silva

Examples

data(filt.se)
tfs <- sample(rownames(filt.se), size = 50, replace = FALSE)
grn_edges <- grn_infer(filt.se, method = "clr", regulators = tfs)
p <- plot_grn(grn_edges, ranked = FALSE)