plotGoAncestors: Plot GO term ancestors

In FGNet: Functional Gene Networks derived from biological enrichment analyses

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")

FGNet documentation built on Nov. 8, 2020, 5:43 p.m.