clusterVisualHeatmap-class {goCluster} | R Documentation |
The class will prepare the goCluster
-result for visualization.
The class provides a wrapper around the
prepareHeatmap
-function. Please read the corresponding
documentation for further details.
prepared
:"list"
, matches the
"tree" structure of the annotation term selection from the
significance analysis. But instead of a single annotation term
each node holds a combination of the annotation term, the genes
that were responsible for the selection of this annotation term and
the expression values of these genes.
Additional slots are described in the documentation of the
clusterVisual-class
and clusterModule-class
.
Class "clusterVisual"
, directly.
Class "clusterModule"
, by class "clusterVisual"
.
signature(object = "clusterVisualHeatmap")
:
interactive setup of the class. There are no options that you can
set on this class.signature(object = "clusterVisualHeatmap")
:
returns the configuration of the object as a list. Since there are
no options to this class, this is always an empty list. signature(object = "clusterVisualHeatmap")
:
non-interactive setup of the class. Not necessary since this class
has no options.signature(object = "clusterVisualHeatmap")
:
prepares the selected annotation terms for the visualization. signature(object = "clusterVisualHeatmap")
:
resets the results of this class so that the analysis can be run
again. signature(object = "clusterVisualHeatmap")
:
generates the actual graphic for this object. signature(x = "clusterVisualHeatmap")
: prints
generic information about the object. Gunnar Wrobel, http://www.gunnarwrobel.de.
prepareHeatmap
,
goCluster-class
,
clusterModule-class
,
clusterVisual-class
set.seed(1000) data(benomylsetupsmall) benomylsetupsmall$classvisu <- "clusterVisualHeatmap" a <- new("goCluster") execute(a) <- benomylsetupsmall if(interactive()){ ## This example can only be run in an interactive mode ## This plot shows only four genes since the loaded dataset ## has been reduced to only 100 genes. Try the same with ## the full dataset display(a, selection = "GO:0003735") }