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]