termGraphs: Extraction and Plotting of GO Terms from a GOHyperGResult...
In Bioconductor/GOstats: Tools for manipulating GO and microarrays

View source: R/GOHyperGResult-accessors.R

termGraphs

R Documentation

Extraction and Plotting of GO Terms from a GOHyperGResult Object

Description

These functions extract and plot graph instances representing the relationships among GO terms tested using hyperGTest.

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.

Details

termGraphs: returns a list of 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).
inducedTermGraph: returns a 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).
plotGOTermGraph: Create a plot using Rgraphviz of a 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.