plotGoAncestors {FGNet} | R Documentation

## Plot GO term ancestors

### Description

Plots the ancestors in the tree ontology for the given GO terms.

### Usage

    plotGoAncestors(goIds, tColor = NULL, ontology = NULL,
        plotOutput = "static", nCharTerm = 50, nSize = NULL, labelCex = NULL,
        asp = NULL, fileName = NULL, height = 1000)

### Arguments

`goIds` | character vector. GO IDs of the terms to plot.
`tColor` | character. Color for the term (i.e. based on expression).
`ontology` | character. If character determines which ontology to plot ("BP"", "MF" or "CC"").
`plotOutput` | "static", "dynamic" or "none". "static" will generate a standard R plot. "dynamic" will produce an interactive tkplot. "none" will not plot the network.
`nCharTerm` | numeric. Max term size (number of characters). Longer terms will be trimmed.
`nSize` | numeric. Determines the node size.
`labelCex` | numeric. Determines the node label size.
`fileName` | character. If provided, the plot is saved as png with this fileName.
`asp` | character. If fileName is provided, asp argument for plot.
`height` | numeric. If fileName is provided, height argument for png().

### Value

An invisible list with the nodes identified as leaves (`leaves`) and the graph (`iGraph`).

### See Also

Overview of the package: `FGNet`

Package tutorial: `vignette("FGNet-vignette")`

### Examples

    plotGoAncestors(c("GO:0000152","GO:0043234", "GO:0044446", "GO:0043227"))

    # plotGoAncestors(c("GO:0051603", "GO:0019941", "GO:0051128","GO:0044265"), plotOutput="dynamic")

    # From analysis:
    txtFile <- paste(file.path(system.file('examples', package='FGNet')),
        "DAVID_Yeast_raw.txt", sep="/")
    results <- format_david(txtFile, jobName="DavidAnalysis")

    plotGoAncestors(getTerms(results, returnValue="GO")$"Cluster 7", ontology="MF")

[Package FGNet version 3.22.1 Index]