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 `ExpressionSet`.

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.db`) 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 version of `hgu95av2.db` was 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.db") &&
           require("fibroEset")) {
           data(integrinMediatedCellAdhesion)
               data(IMCAEntrezLink)
           data(fibroEset)
           attrs <- getDefaultAttrs()
           attrs$graph$rankdir <- "LR"
           plotExpressionGraph(IMCAGraph, IMCAEntrezLink,
                               exprs(fibroEset)[,1],
                               hgu95av2ENTREZID, attrs = attrs)
       }

[Package geneplotter version 1.20.0 Index]