plot-methods {Rgraphviz} | R Documentation

## Plot a graph object - methods

### Description

A plot method for `graph` objects.

### Usage

    ## S4 method for signature 'graph,ANY'
    plot(x, y, ..., name = "", subGList = list(),
        attrs = list(), nodeAttrs = list(), edgeAttrs = list(),
        recipEdges = c("combined", "distinct"))
    ## S4 method for signature 'Ragraph,ANY'
    plot(x, y, edgeAttrs = list(), ..., main = NULL,
        cex.main = NULL, col.main = "black", sub = NULL, cex.sub = NULL,
        col.sub = "black", drawNode = drawAgNode, xlab, ylab, mai)

### Arguments

`x` | The `graph` object to plot
`y` | The layout method to use: One of `dot`, `neato`, `twopi`, `circo`, and `fdp`. The default is `dot`
`name` | The name of the graph, passed to `agopen`
`subGList` | A list of subgraphs taken from the primary `graph` object to be plotted. If provided, these subgraphs will be clustered visually. If not provided, no clusters will be used.
`attrs` | A list of Graphviz attributes to be sent to the layout engine
`nodeAttrs` | A list of attributes for specific nodes
`edgeAttrs` | A list of attributes for specific edges
`recipEdges` | Determines how to draw reciprocating edges. See `agopen`
`main, cex.main, col.main` | Main label and graphic parameters for the plot
`sub, cex.sub, col.sub` | Subtitle and graphic parameters for the plot
`drawNode` | Function to draw the nodes. The default is `drawAgNode`
`xlab` | Label for the x axis of the plot
`ylab` | Label for the y axis of the plot
`mai` | Margins for plot
`...` | General commands to be sent to plot

### details

The first plot method in the `usage` section corresponds to the `graph` class in the `graph` package. It will convert the `graph` object into an object of class `Ragraph` by using Graphviz to perform the layout. Then it will call the plot method for `Ragraph`. The `plot.graph` method is nothing more then a wrapper that calls `agopen` and `plot.Ragraph`.

The second plot method in the `usage` section is for the `Ragraph` class, which describes a Graphviz structure of a graph. This method will extract necessary information from the object and use it to plot the graph.

Users can specify arbitrary drawing functions for the nodes of the `Ragraph` with the `drawNode` argument, although caution is urged. The default drawing function for all nodes is `drawAgNode`, which will draw a basic circle, ellipse or rectangle according to the layout specifications for each node. If supplying a custom function, users are encouraged to look at the code of this function for a more clear picture of the information required to properly draw a node. Users can specify either one custom function to be used for all nodes or a list (where length is equal to the nubmer of nodes) of functions where the Nth element in the list provides the drawing function for the Nth node, and every function will take four parameters - the first is an object of class `AgNode` representing the node itself and the second is an object of class `xyPoint` representing the upper right corner of the Graphviz plotting region (where the lower left is `0,0`). The third parameter, `attrs` is a node attribute list and represents post-layout attribute changes where the user wants to override values present in the layout. The last argument, `radConv` is a divisor to the radius and is used to convert from `Graphviz` units to R plotting units. Outside of the first argument, the rest of these (particularly `radConv` which generally shouldn't be specifically set) do not need to be set by the user, but any drawing function must have them as parameters.

The `attrs` list requires a particular format. It must be of length 3 with names `graph`, `node`, and `edge`. Each of these elements themselves are lists - such that an element of `graph` corresponds to a graph element. A full listing of attributes and their possible settings is available at `http://www.research.att.com/~erg/graphviz/info/attrs.html`. All attribute values should be entered as character strings (even if the requested value is to be otherwise).

The `nodeAttrs` list is used to specify attributes on a particular node, instead of for all nodes. The format of this list is such that the elements correspond to attributes (the name of the element is used to note which attribute) and each element contains a named vector. The names of the vector denote which nodes are having this attribute set and the values in the vector specify the value.

The `edgeAttrs` list is identical in format to `nodeAttrs`. However, the name of the edges is in a particular format where an edge between x and y is named `x~y`. Note that even in an undirected graph that `x~y` is not the same as `y~x` - the name must be in the same order that the edge was defined as having.

### value

The `Ragraph` object used for plotting

### author

Jeff Gentry

### seealso

`graphNEL-class`, `graph-class`

### Examples

    #  WHY DOES THIS NOT WORK IN CHECK?
    #  V <- letters[1:10]
    #  M <- 1:4
    #  g1 <- randomGraph(V, M, .2)
    #  plot(g1)

[Package Rgraphviz version 2.32.0 Index]