Usage
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", ...)Arguments
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.