RamiGO (version 1.18.0)

adjM2gml: Create GML file from readAmigoDot output.

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.

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")