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, nodeLLmap, exprs, LOCUSIDenvir, mapFun, log = FALSE, nodeAttrs = list(), ...)

### Arguments

`graph` | The graph to plot
`nodeLLmap` | A list with element names being node names and the elements being LocusLink IDs corresponding to those node names.
`exprs` | A vector of expression data, with names being Affymetrix IDs and values being the expression level.
`LOCUSIDenvir` | An environment mapping Affymetrix IDs to LocusLink IDs, such as the ones provided in the xxx2LOCUSID 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 `nodeLLmap` parameter is a list that maps the nodes of the graphs to LocusLink IDs. An example of this is the `IMCALocusLink` 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 `LOCUSIDenvir` environment maps Affymetrix IDs to LocusLink 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 `xxx2LOCUSID`, 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.

### Author(s)

Jeff Gentry

### See Also

`plot.graph`, `integrinMediatedCellAdhesion`

### Examples

       if ((require("Rgraphviz")) && (require("hgu95av2")) &&
            (require("fibroEset")) && (interactive())) {
                data(integrinMediatedCellAdhesion)
                data(fibroEset)
                attrs=getDefaultAttrs()
                attrs$graph$rankdir <- "LR"
                plotExpressionGraph(IMCAGraph, IMCALocusLink,
                                    exprs(fibroEset)[,1],
                                    hgu95av2LOCUSID, attrs=attrs)
       }

[Package geneplotter version 1.8.0 Index]