plot_ppi {BioNERO} | R Documentation

## Plot protein-protein interaction network from edge list

### Description

Plot protein-protein interaction network from edge list

### Usage

    plot_ppi(
      edgelist_int,
      color_by = "community",
      clustering_method = igraph::cluster_infomap,
      show_labels = "tophubs",
      top_n_hubs = 5,
      interactive = FALSE,
      add_color_legend = TRUE,
      dim_interactive = c(600, 600)
    )

### Arguments

`edgelist_int` | Data frame containing the edge list for the PPI network. First column is the protein 1 and second column is the protein 2. All other columns are interpreted as edge attributes.
`color_by` | How should nodes be colored? It must be either "community" or a 2-column data frame containing proteins in the first column and a custom annotation in the second column. If "community", a clustering algorithm will be applied. Default: "community".
`clustering_method` | igraph function to be used for community detection. Available functions are cluster_infomap, cluster_edge_betweenness, cluster_fast_greedy, cluster_walktrap, cluster_spinglass, cluster_leading_eigen, cluster_louvain, and cluster_label_prop. Default is cluster_infomap.
`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.
`add_color_legend` | Logical indicating whether to add a color legend for nodes. Default: TRUE.
`dim_interactive` | Numeric vector with width and height of window for interactive plotting. Default: c(600,600).

### Value

A ggplot object.

### Author(s)

Fabricio Almeida-Silva

### See Also

`as_data_frame`,`degree`,`simplify`,`gorder` `igraph_to_networkD3`,`forceNetwork`

### Examples

    ppi_edges <- igraph::get.edgelist(igraph::barabasi.game(n=50, directed=FALSE))
    p <- plot_ppi(ppi_edges, add_color_legend = FALSE)

[Package BioNERO version 1.0.4 Index]