termGraphs {GOstats} | R Documentation |
These functions extract and plot 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", ...)
r |
A GOHyperGResult object as returned by
hyperGTest when given a GOHyperGParams object as
input. |
id |
A character vector of category IDs that specifies which terms should be included in the graph. |
pvalue |
Numeric p-value cutoff to use for selecting category
terms to include. Will be ignored if id is present. |
use.terms |
Logical value indicating whether a "term" node
attribute should be added to the returned graph providing the more
descriptive, but possibly much longer, GO Terms. |
children |
A logical value indicating whether to include direct
child terms of the terms specified by id . |
parents |
A logical value indicating whether to include direct
parent terms of the terms specified by id . |
g |
A graph object as returned by inducedTermGraph
or termGraphs . |
add.counts |
A logical value indicating whether category size counts should be added to the node labels when plotting. |
max.nchar |
The maximum character length for node labels in the plot. |
node.colors |
A named character vector of length two with
compoents sig and not , giving color names for the
significant and non-significant nodes, respectively. |
node.shape |
This argument controls the shape of the plotted nodes and must take on a value allowed by Rgraphviz. |
... |
For 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.
Seth Falcon