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RamiGO (version 1.18.0)

AmiGO visualize R interface

Description

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.

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Version

Version

1.18.0

License

Artistic-2.0

Maintainer

Markus Schroeder

Last Published

February 15th, 2017

Functions in RamiGO (1.18.0)

AmigoDot-class

Class "AmigoDot"
c5.go.mapping

MSigDB C5 GO term to GO ID mapping
AmigoDot.to.graphNEL

Converts an AmigoDot S4 object to a graphNEL object.
readAmigoDot

Parser for the GraphViz DOT format.
exportCytoGML

Writes out an igraph graph to a Cytoscape readable GML file.
RamiGO

AmiGO visualize R interface
igraph-class

Class "igraph"
adjM2gml

Create GML file from readAmigoDot output.
getAmigoTree

Getting the DAG GO tree for a set of GO ID's.
AmigoDot.to.graphAM

Converts an AmigoDot S4 object to a graphAM object.
AmigoDot

AmigoDot constructor and accessors
AmigoDot.to.Cyto

Opening the AmigoDot graph in Cytoscape through RCytoscape.