splitg.mst {netbiov} | R Documentation

## Network plot

### Description

Modular layout style:

A large complex network is plotted by splitting it into its modules. The positions of the vertices in each subnetwork are determined by using the fruchterman-reingold algorithm or the Kamada-kawai algorithm for the minimum spanning tree of each subnetwork. The edges of the minimum spanning tree are shown in black color.

### Usage

    splitg.mst(x,layout.function=NULL, mod.list=NULL,
    colors=NULL,mst.edge.col="white",
    vertex.color = c("red","green","blue","orange"),
    random.v.color=FALSE,in.con.ed.col=NULL,tkplot=FALSE,
    v.size=2, e.size=.5, mst.e.size=1, v.lab=FALSE,
    bg="black", v.lab.cex=0.5, e.lab.cex=0.5,
    v.lab.col="skyblue", lab.dist=0, v.sf=4, sf.modules = 5, ...)

### Arguments

`x` | `x` is a graph object, created using igraph package.
`layout.function` | is a 'function' class or a vector of functions to plot the layout of each module by a function in 'layout.function'.
`mod.list` | `mod.list` is a list object, which provides a modular information about the graph, each components of mod.list contains a vector of nodes to be plotted.
`v.size` | is a numeric value or a numeric vector which contains values to assign the size of the nodes.
`e.size` | is a numeric value to assign the width to edges.
`e.lab.cex` | is a numeric variable; this determines the size of the labels of the vertices or the modules.
`lab.dist` | is a numeric variable; this adjusts labels of vertices.
`sf.modules` | is an integer variable is used to scale up or scale down the graph plot.
`v.sf` | is a numeric value. This is used to adjust vertex size when `v.size` input is a numeric vector.
`mst.edge.col` | This option assigns a color to the edges of the minimum spanning tree of each module of graph 'g'. The default color is black for 'tkplot=TRUE'. If 'tkplot=FALSE' it is white.
`random` | `random` is a logical value, this option is used to choose nodes of split graphs randomly
`colors` | `colors` is a vector of colors. This option is a vector of the edge colors to assign colors to the edges of the graph.
`vertex.color` | `vertex.colors` is a vector of colors to assign colors to the vertices of the modules of the graph.
`random.v.color` | is a logical value, this option is used to assign colors to the vertices colors of the modules, colors for modules are picked randomly.
`in.con.ed.col` | is a scaler, assign colors to the edges which are showing connections between the modules.
`tkplot` | it is a boolean variable, if it is true function will use tkplot function to plot a graph, if it is false function will use plot function with a black background.
`mst.e.size` | is a numeric value which assigns the edge width to the edges of minimum spanning tree of the input graph.
`v.lab` | is a logical value to show vertex label.
`v.lab.cex` | is a numerical value to set the font size of vertex labels.
`v.lab.col` | is a hexadecimal character value to assign colors to vertex labels.
`sf` | is a numeric value. This is used to adjust vertex size when `v.size` input is a numeric vector.
`bg` | is a color value for background.
`...` | `...` parameter for other inputs.

### Value

This function plots a graph using 'tkplot' function available in the 'igraph'. This function returns a list,first component of list is a graph object, second component of the list contains x and y coordinates, third component of list contains color ids of edges of the graph etc.

### Examples

      data("PPI_Athalina")
      data("modules_PPI_Athalina")
            id <- splitg.mst(g1, mod.list=lm, random.v.color=TRUE, tkplot=FALSE )

[Package netbiov version 1.16.0 Index]