plot_grn: Plot gene regulatory network from edge list

In almeidasilvaf/BioNERO: Biological Network Reconstruction Omnibus

Plot gene regulatory network from edge list

Description

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(s)

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)

almeidasilvaf/BioNERO documentation built on Oct. 9, 2024, 1:49 a.m.