inst/visu/components/d3-plugins/graph/README.md

In jwist/visualizeR: visualize metabolomics data interactively

d3.graph

This plugin is not currently in active development.

For a more complete set of graph analysis tools, see the work of Elijah Meeks and Maya Krishnan.

A plugin for manipulating graph data structures.

Todo

• link nodes by name. see this discussion on the force layout

• adjacency list

• graph traversal
• hypergraph

Matrix

Create a matrix

  var matrix = d3.graph.matrix([
    [1,1,0],
    [0,0,0],
    [2,1,1]
  ]);

Get an edge value

matrix(i,j)

Check if edge exists (non-zero)

matrix.has(i,j)

Set an edge value

matrix.set(i,j,value)

Remove an edge

matrix.remove(i,j)

Get outgoing edge indices

matrix.outE(i)

Get incoming edge indices

matrix.inE(i)

todo

• documentation
• changing size

Basics

Convert matrix to list

d3.graph.matrixToList([
  [0,1,0],
  [1,0,0],
  [1,1,1]
])
/*
[
  {"source":0,"target":0,"value":0},{"source":0,"target":1,"value":1},{"source":0,"target":2,"value":0},
  {"source":1,"target":0,"value":1},{"source":1,"target":1,"value":0},{"source":1,"target":2,"value":0},
  {"source":2,"target":0,"value":1},{"source":2,"target":1,"value":1},{"source":2,"target":2,"value":1}
]
*/

Convert list to matrix

d3.graph.listToMatrix([
  {"source":0,"target":1,"value":1},
  {"source":1,"target":0,"value":1},
  {"source":2,"target":0,"value":1},
  {"source":2,"target":1,"value":1},
  {"source":2,"target":2,"value":1}
])
/*
  [0,1,0],
  [1,0,0],
  [1,1,1]
*/

Stateful Use

var graph = d3.graph();

Load a matrix

graph.matrix([
  [0,1,0],
  [1,0,0],
  [1,1,1]
]);

Get the graph as list of links

graph.links();

Get the graph as matrix

graph.matrix();

Nodes and links can be modified by passing in a value. This will overwrite existing data.

graph.nodes(['red', 'purple', 'orange']);
graph.links([{"source":0,"target":0,"value":0},{"source":0,"target":1,"value":1},{"source":0,"target":2,"value":0}]);

Get a description of the graph

graph.description();
// "d3.graph with 3 nodes and 9 links"

jwist/visualizeR documentation built on Dec. 1, 2019, 5:11 p.m.