termGraphs {GOstats} | 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.

### Author(s)

Seth Falcon

[Package GOstats version 2.4.0 Index]