RamiGO: AmiGO visualize R interface
Version 1.22.0

R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.

AuthorMarkus Schroeder, Daniel Gusenleitner, John Quackenbush, Aedin Culhane, Benjamin Haibe-Kains
Bioconductor views Classification GO GraphAndNetwork ThirdPartyClient Visualization
Date of publicationNone
MaintainerMarkus Schroeder <markus.schroeder@ucdconnect.ie>
LicenseArtistic-2.0
Version1.22.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RamiGO")

Getting started

Package overview

Popular man pages

AmigoDot: AmigoDot constructor and accessors
AmigoDot.to.Cyto: Opening the AmigoDot graph in Cytoscape through RCytoscape.
AmigoDot.to.graphAM: Converts an AmigoDot S4 object to a graphAM object.
c5.go.mapping: MSigDB C5 GO term to GO ID mapping
exportCytoGML: Writes out an igraph graph to a Cytoscape readable GML file.
getAmigoTree: Getting the DAG GO tree for a set of GO ID's.
readAmigoDot: Parser for the GraphViz DOT format.
See all...

All man pages Function index File listing

Man pages

adjM2gml: Create GML file from readAmigoDot output.
AmigoDot: AmigoDot constructor and accessors
AmigoDot-class: Class "AmigoDot"
AmigoDot.to.Cyto: Opening the AmigoDot graph in Cytoscape through RCytoscape.
AmigoDot.to.graphAM: Converts an AmigoDot S4 object to a graphAM object.
AmigoDot.to.graphNEL: Converts an AmigoDot S4 object to a graphNEL object.
c5.go.mapping: MSigDB C5 GO term to GO ID mapping
exportCytoGML: Writes out an igraph graph to a Cytoscape readable GML file.
getAmigoTree: Getting the DAG GO tree for a set of GO ID's.
igraph-class: Class '"igraph"'
RamiGO-package: AmiGO visualize R interface
readAmigoDot: Parser for the GraphViz DOT format.

Functions

AmigoDot Man page
AmigoDot-class Man page
AmigoDot.to.Cyto Man page Source code
AmigoDot.to.graphAM Man page Source code
AmigoDot.to.graphNEL Man page Source code
RamiGO Man page
adjM2gml Man page Source code
adjMatrix Man page
adjMatrix,AmigoDot-method Man page
adjMatrix<- Man page
adjMatrix<-,AmigoDot-method Man page
agraph Man page
agraph,AmigoDot-method Man page
agraph<- Man page
agraph<-,AmigoDot-method Man page
annot Man page
annot,AmigoDot-method Man page
annot<- Man page
annot<-,AmigoDot-method Man page
c5.go.mapping Man page
exportCytoGML Man page Source code
getAmigoTree Man page Source code
igraph-class Man page
leaves Man page
leaves,AmigoDot-method Man page
leaves<- Man page
leaves<-,AmigoDot-method Man page
readAmigoDot Man page Source code
relations Man page
relations,AmigoDot-method Man page
relations<- Man page
relations<-,AmigoDot-method Man page

Files

.BBSoptions
DESCRIPTION
NAMESPACE
NEWS
R
R/AmigoDot-Class.R
R/AmigoDot.to.Cyto.R
R/AmigoDot.to.graphAM.R
R/AmigoDot.to.graphNEL.R
R/adjM2gml.R
R/exportCytoGML.R
R/getAmigoTree.R
R/readAmigoDot.R
build
build/RamiGO.pdf
build/vignette.rds
data
data/c5.go.mapping.rda
inst
inst/CITATION
inst/doc
inst/doc/RamiGO.R
inst/doc/RamiGO.Rnw
inst/doc/RamiGO.pdf
man
man/AmigoDot-class.Rd
man/AmigoDot.Rd
man/AmigoDot.to.Cyto.Rd
man/AmigoDot.to.graphAM.Rd
man/AmigoDot.to.graphNEL.Rd
man/RamiGO-package.Rd
man/adjM2gml.Rd
man/c5.go.mapping.Rd
man/exportCytoGML.Rd
man/getAmigoTree.Rd
man/igraph-class.Rd
man/readAmigoDot.Rd
vignettes
vignettes/RamiGO.Rnw
vignettes/cyto.png
RamiGO documentation built on May 20, 2017, 9:45 p.m.

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