Plot Gene Ontology Annotation and Abundance


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Documentation for package ‘PloGO’ version 2.0

Help Pages

abundancePlot Function to summarize and plot abundance information from an annotations results list
aggregateAbundance Function to aggregate the abundance by the group provided
annotationPlot Function to summarize and plot extracted GO annotation
Children Function to extract the children
compareAnnot Function to compare annotation percentages
countAndAbundance Function to do a side by side annotation and abundance plot
Error Error
extract.param Function to extract a parameter from the metatable
extractPairs Extract annotation and abundance side by side for two files
genWegoFile Function to generate a format in Wego native style from a list of Uniprot identifiers
getGoID Function to map a vector of GO terms to the corresponding GO ID's
GOGraphWrapper Simple wrapper for GOGraph
GOParent Function to find the first parent of a GO node
GOTermList Function to extract a list of GO terms at level 2,3 or 4 of the GO hierarchy
inGraph Function to decide if a particular term is in a graph
PloGO Function to do steps of GO annotation and annotation/abundance plots
plotMat A levelplot of abundance by GO category
processAnnotation Function to process a set of annotation files given a list of GO identifiers of interest
processAnnotFile Function to process a single file in wego-like native format
processGoFile Function to process a single file in wego-like native format
processPlainAnnotation Function to process a set of annotation files given a list of identifiers of interest
read.annot.file Function to read an annotation file.
readMeta Utility function to process metafile
writeAnnotation Function to print GO annotation to files
writeGOannot Function to write annotation out to a file