order of networkx nodes - print graphviz layout vertically

Question

I have a graphviz layout I've created. I've also tried to create graphs using differing drawing styles such as random, circular, shell, spectral, spring. I believe graphviz is the most accurate to my data. I created a file containing two columns of strings. These columns are the edges. (Each string has at least one corresponding partner, which is why GraphViz layout I think best represents these data) From that file I created a list of unique strings for the nodes. I then plotted the nodes and added the edges. A version of my script can be found here: ( networkx - change node size based on list or dictionary value )

Here is the output using graphviz layout (instead of 100 the sizes were multiplied by 10, some numbers are as high as 15020, and other as small as 10):

Here is the output using random:

Can one conclude that all the edges that should be present are present in the graphviz example? Is it correct to say that smaller nodes "on top of" larger ones are conncted? Is it possible to make their edges viewable? Are there so many more edge visible in the random example due to the random placement of nodes in the graph, therefore edges can have a much higher 'length' to traverse?

If what I think is correct, and the graphviz is the best drawing option for my data, since there are many overlaps between the nodes and edges (and if those nodes "on top of" the larger node are indeed connected) what I would like to do is sort the plot in a "vertical" fashion. So, the largest nodes with most edges on top, going down to nodes with only 1 edge. I've tried to change the overall figure size, which did not make anything more discernable. For some reason, I got the original window with the plot and a secondary window with a grey blank background.

So, I'm starting to think some of my assumptions are correct. Here is the image as large as I can make it:

Answer 1

What is happening is that networkx puts the nodes over top of the edges. So the edges are drawn underneath the nodes.

I believe the easiest way to still see them is to set alpha=0.5 or something else less than 1 in the draw command to make the nodes partly transparent.