PlotGraphviz.jl

• PlotGraphviz.jl tries to unleash the power of Graphviz in your IJulia environment. It is using ShowGraphviz.jl, which derive various show methods from text/vnd.graphviz (https://graphviz.org). To parse dot files it uses ParserCombinator.jl.

• PlotGraphviz.jl presents a simple interface for (nearly) all features of Graphviz.

• PlotGraphviz.jl accepts graphs from SimpleWeightedGraphs.jl

Installation

Installation is straightforward: enter Pkg mode by hitting ], and then

(@v1.7) pkg> add PlotGraphviz

How to use it

Generate some graphs by importing Graphs.jl or SimpleWeightedGraphs.jl:

using Graphs, SimpleWeightedGraphs

using PlotGraphviz

and use SimpleWeightedGraphs.jl to generate a simple graph:

g = SimpleWeightedGraph(3)  # or use `SimpleWeightedDiGraph` for directed graphs
SimpleWeightedGraphs.add_edge!(g, 1, 2, 0.5)
SimpleWeightedGraphs.add_edge!(g, 2, 3, 0.8)
SimpleWeightedGraphs.add_edge!(g, 1, 3, 2.0);

plot_graphviz(g)

You can use generators from Graphs.jl, i.e.:

grid = Graphs.grid([10,5])

{50, 85} undirected simple Int64 graph

plot_graphviz(SimpleWeightedGraph(grid))

Importing and modifying graphs

First, let us take a standard example, and use the function read_dot_file (more with ? function) to import the graph from a dot-file.

mk, attrs = read_dot_file("./test/data/directed/clust4.gv");

plot_graphviz(mk, attrs)

The value $attrs$ is a struct, that stores the GraphvizAttributes of the imported graph (as it is defined in "*.dot" file itself)

There are mainly 3 different graph options available in Graphviz (see website for more):

• graph_options: attributes/properties, which belongs to the complete graph (i.e. rankdir, label, ...)
• node_options: attributes/properties to modify all nodes at once
• edge_options: attributes/properties to modify all edges at once

As an example we would like to modify the shape of all nodes. Therefore we use the set! function. As we would like to modify the nodes, we have to use the node_options of our struct:

set!(attrs.node_options, Property("shape","box"));
plot_graphviz(mk, attrs)

Next we change the orientation of our graph by modifying its graph_options and additionally we change the edge color (using edge_options):

set!(attrs.graph_options, Property("rankdir","LR"));
set!(attrs.edge_options, Property("color","blue"));
plot_graphviz(mk, attrs; scale = 5)

To modify a single node, we need to access the node by its $name (String)$ or its $id (Int)$:

set!(attrs.nodes, "a0", Property("shape","triangle"))
set!(attrs.nodes, "a0", Property("filled","true"))
set!(attrs.nodes, "a0", Property("color","yellow"))
plot_graphviz(mk, attrs; scale = 5)

To access a single edge, we have to know its unique $id (Int)$. We can use get_id to return the id from a node with a given name.

id_a0 = get_id(attrs.nodes,"start");
id_a1 = get_id(attrs.nodes,"a0");

set!(attrs.edges,id_a0, id_a1, Property("color","red"))
set!(attrs.edges,id_a0, id_a1, Property("xlabel","2.0"))
set!(attrs.edges,id_a0, id_a1, Property("fontsize","8.0"))
plot_graphviz(mk, attrs; scale = 5)

The imported graph $mk, attrs$ consists of two subgraphs (of type cluster - see Graphviz). To get access to their attributes we need to change the cluster itself.

set!(attrs.subgraphs[1].graph_options, Property("color","Turquoise"));
set!(attrs.subgraphs[1].graph_options, Property("label","process #NEW 1"));
plot_graphviz(mk, attrs; scale = 5)

But it is not possible to access a node or edge inside a cluster. Therefore we can use a built-in trick to manipulate the node directly:

set!(attrs.subgraphs[2].nodes, "b0", Property("color","green")); ## does not work inside a cluster!
set!(attrs.nodes, "b0", Property("color","green")); ## but this works!
plot_graphviz(mk, attrs; scale = 5)

To write and store the graph use the write_dot_file function:

write_dot_file(mk,"./test.dot"; attributes=attrs);

Default Attributes:

Back to our graph $g$. How to get the Graphviz attributes of this graph? Well, there are two ways:

1. call an empty constuctor: attrs = GraphivzAttributes()
2. call the contructor with our graph $g$: attrs = GraphivzAttributes(g::AbstractSimpleWeightedGraph)

The second call generates the default plotting parameter, which ist used to represent the graph using plot_graphviz().

attrs = GraphvizAttributes(g)

GraphvizAttributes(Property[Property{String}("weights", "false"), Property{String}("largenet", "200")], Property[Property{String}("center", "\"1,1\""), Property{String}("overlap", "scale"), Property{String}("concentrate", "true"), Property{String}("layout", "neato"), Property{String}("size", "3.0")], Property[Property{String}("color", "Turquoise"), Property{String}("fontsize", "7.0"), Property{String}("width", "0.25"), Property{String}("height", "0.25"), Property{String}("fixedsize", "true"), Property{String}("shape", "circle")], Property[Property{String}("arrowsize", "0.5"), Property{String}("arrowtype", "normal"), Property{String}("fontsize", "1.0")], PlotGraphviz.gvSubGraph[], gvNode[gvNode(1, "1", Property[]), gvNode(2, "2", Property[]), gvNode(3, "3", Property[])], gvEdge[gvEdge(1, 2, Property[Property{Float64}("xlabel", 0.5)]), gvEdge(1, 3, Property[Property{Float64}("xlabel", 2.0)]), gvEdge(2, 1, Property[Property{Float64}("xlabel", 0.5)]), gvEdge(2, 3, Property[Property{Float64}("xlabel", 0.8)]), gvEdge(3, 1, Property[Property{Float64}("xlabel", 2.0)]), gvEdge(3, 2, Property[Property{Float64}("xlabel", 0.8)])])

Color and Path:

There a two special functions available.

Color the graph:

One typical problem in graph theory is to identify connected components and to color them:

g2,attrs2 = read_dot_file("./test/data/example.dot");

plot_graphviz(g2; edge_label=true, scale=6)

Use Graphs.jl algorithm to identify connected components:

L = Graphs.connected_components(g2)

8-element Vector{Vector{Int64}}:
 [1, 19]
 [2, 7, 13, 16]
 [3, 4, 9, 11]
 [5, 6, 10, 17, 18]
 [8, 20]
 [12]
 [14]
 [15]

Transform it to a vector for which each number represents the color of node:

color_vec = zeros(Int, 1, nv(g2))
color = 1
for components in L
    for idx in components
        color_vec[idx] = color
    end
    color = color + 1
end

plot_graphviz(g2, attrs2; colors = color_vec, scale = 7)

Shortest path:

Import a small layered dag:

lydag, attrs = read_dot_file("./test/data/small_layered_dag.dot");

plot_graphviz(lydag; landscape = true, scale = 7)

To get the shortest path, we use Graphs.jl:

path = Graphs.dijkstra_shortest_paths(lydag, 3);

# convert precedessor list in path:
spath(ds, source, sink) = source == sink ? source : [spath(ds, ds.parents[source], sink) source];

And evaluate shortest path between super-sink and super-source:

L= spath(path, 25, 3)

1×12 Matrix{Int64}:
 3  34  26  31  22  16  28  12  11  27  20  25

And that represents the shortest path in our graph, and we can visualize this by using the $path$ option:

plot_graphviz(lydag; landscape = true, scale = 7, path = L)

Comments

Open issues:

• Not all test graphs are imported correcty.
• Performance issues have to be solved.
• Design Patterns and Best Practices to be implemented.
• Tests are missing!