plotExpressionGraph {geneplotter} | R Documentation |
Given a graph and expression data for one entity, will plot the graph with the nodes colored according to the expression levels provided.
plotExpressionGraph(graph, nodeLLmap, exprs, LOCUSIDenvir, mapFun, log = FALSE, nodeAttrs = list(), ...)
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 |
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.
Jeff Gentry
plot.graph
, integrinMediatedCellAdhesion
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) }