plot_grn {BioNERO}R Documentation

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,
  interactive = FALSE,
  layout = igraph::with_kk,
  arrow.gap = 0.01,
  ranked = TRUE,
  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.

interactive

Logical indicating whether the network should be interactive or not. Default is FALSE.

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.

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

See Also

igraph_to_networkD3, forceNetwork geom_edges, geom_nodes, geom_nodetext,theme_blank, geom_nodetext_repel new_scale

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)

[Package BioNERO version 1.0.4 Index]