adjM2gml: Create GML file from readAmigoDot output.

In RamiGO: AmiGO visualize R interface

Description

Takes a part of the output of the readAmigoDot function and creates a GML file by calling exportCytoGML().

Usage

adjM2gml(adjMatrix, edgecolor, vertexcolor,
  nodelabels, nodedescription, filename)

Arguments

adjMatrix	adjacency matrix, parents in rows, children in cols.
edgecolor	character vector of the length of existing edges.
vertexcolor	character vector of the length of existing nodes.
nodelabels	character vector of the length of existing nodes.
nodedescription	character vector of the length of existing nodes.
filename	output filenames.

Author(s)

Markus Schroeder <[e-mail]>

Benjamin Haibe-Kains <[e-mail]>

Examples

## set GO ID's and color
#goIDs <- c("GO:0051130","GO:0019912","GO:0005783")
#color <- c("lightblue","red","yellow")

#dd <- getAmigoTree(goIDs=goIDs,color=color,
#  filename="example",picType="dot",saveResult=FALSE)
#tt <- readAmigoDot(object=dd)

#adjM2gml(adjMatrix(tt),relations(tt)$color,
#  annot(tt)$fillcolor,annot(tt)$GO_ID,
#  annot(tt)$description,"example")

Example output

Loading required package: gsubfn
Loading required package: proto
Warning message:
no DISPLAY variable so Tk is not available 

RamiGO documentation built on May 2, 2018, 3:30 a.m.