printGraph-methods {topGO} | R Documentation

## Visualisation functions

### Description

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

### Usage

    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, ...)

### Arguments

`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.

### Details

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.

### Author(s)

Adrian Alexa

### See Also

`groupStats-class`, `getSigGroups-methods`

### Examples

    ## 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)

[Package topGO version 2.39.1 Index]