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    <p>As @ninjalj points out, one of the neat things about graphviz is, that it allows you to represents graphs nicely and get rid of "flaws" or "imperfections" like overlaps - e.g. by using attributes such as <a href="http://www.graphviz.org/doc/info/attrs.html#d%3aoverlap" rel="nofollow"><code>overlap</code></a> and <a href="http://www.graphviz.org/doc/info/attrs.html#d%3aoverlap_scaling" rel="nofollow"><code>overlap_scaling</code></a>.</p> <p>However, you point out that:</p> <blockquote> <p>I know I can force the x and y positions of nodes and thus induce overlap, but in this case, I am writing a C# program that given certain input spits out the relevant dot script for the graph, so the number of nodes, etc are not hardcoded and so I can't come up with a scheme to hard-code x and y positions of all nodes.</p> </blockquote> <p>So, as I see it, what you say is that you know that when you are given a certain input, you are going to generate a certain graph - in other words, you know the number of nodes ( and clusters ) as a function of the input. This makes me think that @Daniel Kinsman's suggestion might be the way to go for you - that is, implementing your own DOT layout engine for that particular purpose.</p> <p>I do not say that this is simple, however, it is not impossible and the logic needed of course greatly depends on the goal of your application.</p> <p>But before doing any implementation, I think you should have a look at the <a href="http://www.graphviz.org/content/cluster" rel="nofollow"><code>cluster</code> functionality</a> already built into graphviz ( which @Daniel Kinsman also points out ) and think about if it really is worth the extra effort to do a custom DOT layout engine implementation or if the cluster functionality might be sufficient for you.</p>
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    1. POHow to force nodes to overlap by a specified amount in the dot language (graphviz)
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