GOxploreR (version 1.2.8)

visRDAGBP: Species-specific biological process GO-DAG

Description

A sub-dag of biological process terms for a certain species e.g DAG of the gene association GO-terms for Arabidopsis thaliana. The label "J","R" and "L" on the right side of the plot gives the number of connections between the regular node (RN) on the level and the nodes right below it (RN are nodes that have all their children nodes represented in the next level) .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

visRDAGBP(organism, plot = TRUE)

Value

A list containing the plot of the DAG and all the GO terms presents in each node

Arguments

organism

The organism supported by the package. Both the scientific / common name of the organism can be use to derive the Sub-DAG. If this argument is "BP" the reduced BP GO-DAG is visualised.

plot

If TRUE, both the reduced DAG and the GO-terms contained in each node are derived

Examples

# Reduced GO-DAG for Human
visRDAGBP(organism = "Homo sapiens")

# Reduced GO-DAG for Rat
visRDAGBP(organism = "Rat")

# RN GO-terms on level 2 can be access as follows
visRDAGBP(organism = "Human", plot = FALSE)$"L2 RN"

# JN GO-terms on level 16 can be access as follows
visRDAGBP(organism = "Human", plot = FALSE)$"L16 JN"

# LN GO-terms on level 18 can be access as follows
visRDAGBP(organism = "Human", plot = FALSE)$"L18 LN"