plotGoAncestors {FGNet} | R Documentation |
Plots the ancestors in the tree ontology for the given GO terms.
plotGoAncestors(goIds, tColor = NULL, ontology = NULL, plotOutput = "static", nCharTerm = 50, nSize = NULL, labelCex = NULL, asp = NULL, fileName = NULL, height = 1000)
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(). |
An invisible list with the nodes identified as leaves (leaves
) and the graph (iGraph
).
Overview of the package: FGNet
Package tutorial: vignette("FGNet-vignette")
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")