printGraph-methods: Visualisation functions
In ycl6/topGO-Bioc: Enrichment Analysis for Gene Ontology

Description Usage Arguments Details Author(s) See Also Examples

Functions to plot the subgraphs induced by the most significant GO terms

showSigOfNodes(GOdata, termsP.value, firstSigNodes = 10, reverse = TRUE,
               sigForAll = TRUE, wantedNodes = NULL, putWN = TRUE,
               putCL = 0, type = NULL, showEdges = TRUE,  swPlot = TRUE,
               useFullNames = TRUE, oldSigNodes = NULL, useInfo = c("none", "pval", "counts", "def", "np", "all")[1],
               plotFunction = GOplot, .NO.CHAR = 20)

printGraph(object, result, firstSigNodes, refResult, ...)

`object`	an object of class `topGOdata`.
`GOdata`	an object of class `topGOdata`.
`result`	an object of class `topGOresult`.
`firstSigNodes`	the number of top scoring GO terms which ....
`refResult`	an object of class `topGOresult`.
`termsP.value`	named vector of p-values.
`reverse`	the direction of the edges.
`sigForAll`	if `TRUE` the score/p-value of all nodes in the DAG is shown, otherwise only the score for the `sigNodes`
`wantedNodes`	the nodes that we want to find, we will plot this nodes with a different color. The vector contains the names of the nodes
`putWN`	the graph is generated with using the firstSigNodes and the wantedNodes.
`putCL`	we generate the graph from the nodes given by all previous parameters, plus their children. if putCL = 1 than only the children are added, if putCL = n we get the nodes form the next n levels.
`type`	used for ploting pie charts
`showEdges`	if `TRUE` the edge are shown
`swPlot`	if true the graph is ploted, if not no ploting is done.
`useInfo`	aditional info to be ploted to each node.
`oldSigNodes`	used to plot the (new) sigNodes in the same collor range as the old ones
`useFullNames`	argument for internal use ..
`plotFunction`	argument for internal use ..
`.NO.CHAR`	argument for internal use ..
`...`	Extra arguments for `printGraph` can be: `fn.prefix` character string giving the file name prefix. `useInfo` as in `showSigOfNodes` function. `pdfSW` logical attribute switch between PDF or PS formats.

There are two functions available. The showSigOfNodes will plot the induced subgraph to the current graphic device. The printGraph is a warping function for showSigOfNodes and will save the resulting graph into a PDF or PS file.

In the plots, the significant nodes are represented as rectangles. The plotted graph is the upper induced graph generated by these significant nodes.

Adrian Alexa

groupStats-class, getSigGroups-methods

## Not run: 
data(GOdata)
data(results.tGO)

showSigOfNodes(GOdata, score(resultFisher), firstSigNodes = 5, useInfo = 'all')
printGraph(GOdata, resultFisher, firstSigNodes = 5, fn.prefix = "sampleFile", useInfo = "all", pdfSW = TRUE)

## End(Not run)