FGNet (version 3.6.2)

plotGoAncestors: 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")