Plot Gene Ontology and KEGG pathway Annotation and Abundance


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Documentation for package ‘PloGO2’ version 1.10.0

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abundancePlot Function to summarize and plot abundance information from an annotations results list
annotationPlot Function to summarize and plot extracted GO or pathway annotation
compareAnnot Function to compare annotation percentages
ExcelToPloGO Function to add GO annotation to an Excel spread sheet
ExcelToPloPathway Function to add KEGG pathway annotation to an Excel spread sheet
genAnnotationFiles Function to generate a format in Wego native style from a list of Uniprot identifiers
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
GOTermList Function to extract a list of GO terms at level 2,3 or 4 of the GO hierarchy
PloGO Function to do steps of GO annotation and annotation/abundance plots
PloPathway Function to do steps of pathway annotation and annotation/abundance plots
plotAbundanceBar Function to plot abundance barplot
printSummary Function to print the summary file of PloGO2 results.
processAnnotation Function to process a set of annotation files given a list of GO/pathway identifiers of interest
processGoFile Function to process a single file in wego-like native format
processPathFile Function to process a single pathway file in wego-like native format
read.annot.file Function to read an annotation file.
writeAnnotation Function to print GO/pathway annotation to files