Plotting a 3d network model using graph

I want to plot a 3 dimensional network model using the graph function.

for example

edges1 = [1,1,1,2,2,2,2,2,2,2,3,3,3,3,3,3,4,4,4,4,4,5,6,6,6,6,6,7,8,8,8,8,10,11,11,11];
egdes2 = [2,3,4,3,4,5,6,7,8,9,4,5,6,10,11,12,7,8,10,11,13,6,8,9,11,12,14,8,9,11,13,14,11,12,13,14];
x = [0,0,0.5000,0.5000,0,0.5000,0,0.5000,0,1.0000,1.0000,1.0000,1.0000,1.0000];
y = [0,0.5000,0,0.5000,0,0.5000,1.0000,1.0000,1.0000,0,0.5000,0,1.0000,1.0000];
z = [0,0.5000,0.5000,0,1.0000,1.0000,0,0.5000,1.0000,0,0.5000,1.0000,0,1.0000];
G = graph(edges1,egdes2);
plot(G,'Xdata',x,'Ydata',y,'Zdata',z)

However, the line visualization does not give good depth percepsion, and 3d structure can only be percieved when roatating the image.

I'm looking for a way to give the edges some volume to improve visualization, without making the image too heavy to handle.

Is there a neat way to do this?

Thanks!

Answer 1

[ag]

Hi Shahar,

To improve the visualization of a 3D network model in MATLAB and give the edges some volume, you can use cylinders to represent the edges instead of simple lines. This approach can enhance depth perception and make the 3D structure more apparent.

The below code snippet demonstrates how can this be achieved:

% Define the edges and node coordinates
edges1 = [1,1,1,2,2,2,2,2,2,2,3,3,3,3,3,3,4,4,4,4,4,5,6,6,6,6,6,7,8,8,8,8,10,11,11,11];
edges2 = [2,3,4,3,4,5,6,7,8,9,4,5,6,10,11,12,7,8,10,11,13,6,8,9,11,12,14,8,9,11,13,14,11,12,13,14];
x = [0,0,0.5,0.5,0,0.5,0,0.5,0,1,1,1,1,1];
y = [0,0.5,0,0.5,0,0.5,1,1,1,0,0.5,0,1,1];
z = [0,0.5,0.5,0,1,1,0,0.5,1,0,0.5,1,0,1];

% Create the graph
G = graph(edges1, edges2);

% Plot the nodes
figure;
scatter3(x, y, z, 100, 'filled', 'MarkerFaceColor', 'b');
hold on;

% Plot the edges with volume
numEdges = numedges(G);
for i = 1:numEdges
    % Get the start and end points of each edge
    startNode = edges1(i);
    endNode = edges2(i);
    
    % Get coordinates for the start and end nodes
    xStart = x(startNode);
    yStart = y(startNode);
    zStart = z(startNode);
    xEnd = x(endNode);
    yEnd = y(endNode);
    zEnd = z(endNode);
    
    % Create a cylinder between the nodes
    [X, Y, Z] = cylinder(0.02, 8); % Adjust radius for thickness
    Z = Z * sqrt((xEnd - xStart)^2 + (yEnd - yStart)^2 + (zEnd - zStart)^2);
    
    % Rotate and translate the cylinder to the correct position
    [theta, phi, r] = cart2sph(xEnd - xStart, yEnd - yStart, zEnd - zStart);
    R = makehgtform('axisrotate', [0 -1 0], phi, 'axisrotate', [0 0 1], theta);
    for j = 1:numel(X)
        pt = R * [X(j); Y(j); Z(j); 1];
        X(j) = pt(1);
        Y(j) = pt(2);
        Z(j) = pt(3);
    end
    surf(X + xStart, Y + yStart, Z + zStart, 'FaceColor', 'r', 'EdgeColor', 'none');
end

axis equal;
grid on;
xlabel('X');
ylabel('Y');
zlabel('Z');
title('3D Network Model with Volume on Edges');
hold off;

●

For more details, please refer to the following MathWorks documentation:

• Scatter - https://www.mathworks.com/help/matlab/ref/scatter.html
• Cylinder - https://www.mathworks.com/help/matlab/ref/cylinder.html
• makehgtform - https://www.mathworks.com/help/matlab/ref/makehgtform.html
• To enhance the view, you may use camlight - https://www.mathworks.com/help/matlab/ref/camlight.html

Hope this helps!

[shahar goren]

Thank you @ag,

This might be the best approach, but I was looking for a method that can work without adding each edge separately, because this would mean the graphics computations (for example, when rotating the image) will be very slow if the network is large.

Anyhow, Thank you for your answer after all this time!