graph
instances representing the
relationships among GO terms tested using hyperGTest
.
termGraphs(r, id = NULL, pvalue = NULL, use.terms = TRUE)
inducedTermGraph(r, id, children = TRUE, parents = TRUE)
plotGOTermGraph(g, r = NULL, add.counts = TRUE, max.nchar = 20, node.colors=c(sig="lightgray", not="white"), node.shape="plaintext", ...)
GOHyperGResult
object as returned by
hyperGTest
when given a GOHyperGParams
object as
input. id
is present."term"
node
attribute should be added to the returned graph providing the more
descriptive, but possibly much longer, GO Terms.id
.id
.graph
object as returned by inducedTermGraph
or termGraphs
.sig
and not
, giving color names for the
significant and non-significant nodes, respectively.plotGOTermGraph
, extra arguments are passed to
the plot
function.graph
objects each
representing one of the connected components of the subgraph of
the GO ontology induced by selecting the specified GO IDs (if
id
is present) or by selecting the GO IDs that have a
p-value less that pvalue
. If use.terms
is
TRUE
the GO IDs will be translated into GO Term names and
attached to the nodes as node attributes (see nodeData
).
Edges in the graphs go from child (more specific) to parent (less
specific).
graph
object representing
the GO graph induced by the terms specified by id
. The
children
and parent
arguments control whether direct
children and/or direct parents of the terms specified by id
are added to the graph (at least one of the two must be
TRUE
).
graph
object as returned by either termGraphs
or
inducedTermGraph
. If a GOHyperGResult
object is
provided, then the nodes will be colored according to significance
(based on the result object's pvalueCutoff
) and counts will
be added to show the size of the categories.