plot.abstract.nodes {netbiov} | R Documentation

## Exploratory visualization of information spread of biological networks

### Description

Modular layout style:

Visualization of modules in an abstract way. In the function `plot.abstract.nodes`, nodes in a module are replaced by a single node and the relative size of a node is proportional to the total number of nodes in a module. In the functions `plot.abstract.module`, `plot.abstract.nodes`, edges between two modules are replaced by a single edge and the total number of edges between two modules are reflected by the relative edge-width.

### Usage

    ## S3 method for class 'abstract.nodes'
    plot(x, mod.list=NULL,  rest.module=TRUE,
    color.random=FALSE, nodes.color = NULL, edge.colors=NULL,
    layout.function=NULL,tkplot=FALSE,v.sf = 0, e.sf = 0,lab.color=NULL,
    lab.cex=NULL, lab.dist=NULL, bg="black", ... )

### Arguments

`x` | `x` is a graph object created from an adjacency matrix or from a tabular data of two columns using `graph()` function available in `igraph`
`mod.list` | `mod.list` is a list object each components of mod.list consists a vector of module to be plotted.
`random` | is a logical value, if modules information is not provided then random nodes for the modules are selected.
`rest.module` | is a logical value, rest of the nodes to be plotted as a one module (if TRUE) or independently (if FALSE)
`color.random` | is a logical value, if this option is TRUE it will assign random color to each module or nodes.
`nodes.color` | assigns colors to nodes of recreated graph
`edge.colors` | is a vector of colors, assigned to color edges depending on their width from small to large width.
`layout.function` | is a function class, this corrosponds to a layout function given as an input to plot a graph. Input function should return a two column matrix which has same no of rows as the modules in the graph
`tkplot` | is a boolean variable, if it is true function will use this option to plot a graph, if it is false function will use plot function with a black background.
`v.sf` | is a numeric value, this option to increase or decrease the size of nodes
`e.sf` | is a numeric value, this option to increase or decrease width of edges
`lab.color` | colors the vertices and edge labels
`lab.cex` | is anumeric value, increase or decrease the font size of labels
`lab.dist` | is a numeric value, adjust vertex labels
`bg` | is a color value to adjust background color of the plot.
`...` | `...` parameter for other inputs.

### Author(s)

Shailesh Tripathi, Frank Emmert-Streib

### References

http://bio-complexity.com/

### Examples

      require(igraph)
      data("PPI_Athalina")
      data("modules_PPI_Athalina")
      plot.abstract.nodes(g1, mod.list = lm,
    edge.colors = c("red","green","blue","orange"))

[Package netbiov version 1.14.0 Index]