visRsubDAGBP: Visualise the GO-DAG for a specific organism based on certain...

In GOxploreR: Structural Exploration of the Gene Ontology (GO) Knowledge Base

Visualise the GO-DAG for a specific organism based on certain GO-terms

Description

A category in the organism specific DAG is regarded as important if it contains at least one GO-terms from the vector supplied. The function does not visualise the entire organism's DAG, it accepts a range of GO-terms and DAG categories that contains these GO-terms are visualise. We refer to these categories as the important and everything else is faded out. The supported organisms are "Homo sapiens / Human", "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish", "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast", "Schizosaccharomyces pombe / Fission yeast", "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".

Usage

visRsubDAGBP(goterm, organism)

Arguments

goterm	A vector of biological process GO-terms
organism	The organism whose DAG we want to visualise based on the GO-terms supplied. If this argument is "BP" the general reduced GO BP tree is used.

Value

Returns a plot highlighting the important categories i.e. the categories containing the GO-terms of interest

Examples

Terms <- c("GO:0000278", "GO:0006414","GO:0022403","GO:0006415",
"GO:0006614","GO:0045047","GO:0072599","GO:0000279")

# Visualised Human GO-DAG based on the GO-terms given
visRsubDAGBP(goterm = Terms, organism = "Human")

GOxploreR documentation built on Nov. 3, 2023, 5:08 p.m.