plotExpressionGraph {geneplotter} | R Documentation

## A function to plot a graph colored by expression data

### Description

Given a graph and expression data for one entity, will plot the graph with the nodes colored according to the expression levels provided.

### Usage

    plotExpressionGraph(graph, nodeEGmap, exprs, ENTREZIDenvir, mapFun, log = FALSE, nodeAttrs = list(), ...)

### Arguments

`graph` | The graph to plot
`nodeEGmap` | A list with element names being node names and the elements being EntrezLink IDs corresponding to those node names.
`exprs` | A vector of expression data, with names being Affymetrix IDs and values being the expression level.
`ENTREZIDenvir` | An environment mapping Affymetrix IDs to EntrezLink IDs, such as the ones provided in the xxx2ENTREZID environments from the Bioconductor data packages (where xxx) is a data package)
`mapFun` | A function to map expression levels to colors
`log` | Whether or not the expression data
`nodeAttrs` | A list of node attributes, as per `plot.graph`
`...` | Any extra arguments to be passed to `plot.graph`

### Details

This function can be used to plot a graph and have the nodes colored according to expression levels provided by the user. The `graph` parameter is a `graph` object from the `graph` package.

The `nodeEGmap` parameter is a list that maps the nodes of the graphs to EntrezLink IDs. An example of this is the `IMCAEntrezLink` object in the `integrinMediatedCellAdhesion` data set in the `graph` package.

The `exprs` argument is a vector mapping expression levels to Affymetrix IDs. One way to generate an appropriate vector is to extract a single column from an `exprSet`.

The `ENTREZIDenvir` environment maps Affymetrix IDs to EntrezLink IDs. The simplest way to provide this argument is to load the preferred Bioconductor data package (e.g. `hgu95av2`) and pass in that package's `xxx2ENTREZID`, where `xxx` is the name of the package.

The `mapFun` function defaults to the function `defMapFun`, which maps nodes to be either blue, green or red depending for expression ranges of 0-100, 101-500, and 501+. In the case where `log` is `TRUE` these ranges are modified with `log2`. Custom versions of this function can be supplied by the user - it must take two parameters, first the expression vector and a boolean value (`log`) specifying if the data has had a `log2` applied to it. The function must return a vector with the same names as the expression vector, but the values of the vector will be color strings.

The `nodeAttrs` list can be specified if any other node attributes are desired to be set by the user. Please see the `plot.graph` man page for more information on this. The other attribute list (`attrs` and `edgeAttrs`) can be passed in via the `...` parameter.

The IMCAEntrezLink data structure was created for the purpose of illustrating this program. On Sept 24 2007, the current versions of hgu95av2.db and hgu95av2 were used to map from the nodes of IMCAGraph (in graph package) to Entrez identifiers.

### Author(s)

Jeff Gentry

### See Also

`plot.graph`, `integrinMediatedCellAdhesion`

### Examples

       if ((require("Rgraphviz")) && (require("hgu95av2")) &&
            (require("fibroEset")) && (interactive())) {
                data(integrinMediatedCellAdhesion)
                data(IMCAEntrezLink)
                data(fibroEset)
                attrs=getDefaultAttrs()
                attrs$graph$rankdir <- "LR"
                plotExpressionGraph(IMCAGraph, IMCAEntrezLink,
                                    exprs(fibroEset)[,1],
                                    hgu95av2ENTREZID, attrs=attrs)
       }

[Package geneplotter version 1.16.0 Index]