RamiGO (version 1.18.0)

AmigoDot: AmigoDot constructor and accessors

Description

Functions for creating and manipulating AmigoDot-class objects.

Usage

agraph(object)
agraph(object) <- value
adjMatrix(object)
adjMatrix(object) <- value
annot(object)
annot(object) <- value
relations(object)
relations(object) <- value
leaves(object)
leaves(object) <- value

Arguments

object

An AmigoDot S4 object

value

An AmigoDot S4 object

Value

AmigoDot

Object of class AmigoDot.

agraph

igraph object.

adjMatrix

Adjacency Matrix.

annot, leaves

Annotation for each node.

relations

Meta information about the edges between nodes.

Details

agraph(object)Gets the igraph object.

agraph(object) <- valueSets the igraph object.

adjMatrix(object)Gets the adjacency matrix.

adjMatrix(object) <- valueSets the adjacency matrix.

annot(object)Gets the data.frame containing the annotation of the tree with the columns node, GO_ID, description, color, fillcolor and fontcolor.

annot(object) <- valueSets the the data.frame containing the annotation of the tree with the columns node, GO_ID, description, color, fillcolor and fontcolor.

relations(object)Gets the data.frame containing the relations between the node of the tree and also information about the edges. The columns are parent, child, arrowhead, arrowtail, color and style.

relations(object) <- valueSets the the data.frame containing the relations between the node of the tree and also information about the edges. The columns are parent, child, arrowhead, arrowtail, color and style.

leaves(object)Gets the data.frame containing the leaves of the tree with the columns node, GO_ID, description, color, fillcolor and fontcolor.

leaves(object) <- valueSets the the data.frame containing the leaves of the tree with the columns node, GO_ID, description, color, fillcolor and fontcolor.

See Also

AmigoDot-class igraph

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)

agraph(tt)
adjMatrix(tt)
annot(tt)
relations(tt)
leaves(tt)