# Plot Gene Ontology and KEGG pathway Annotation and Abundance

## Documentation for package ‘PloGO2’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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