digraph | Very simple C directed graph library

Now I checked again and I noticed that I put the function to wrong place. I will answer it below.

The reason why the edge weights are plotted is that the weights are not updated after removing a node. Hence, pos and labels in your script should be recalculated after removing the node:

Simply call nx.draw(G, pos, with_labels=True) again before plotting new graph. Your code should look like:

Given the coordinates of two nodes (x1, y1) and (x2, y2) the label position is computed as

Below is a quick hack that could be useful until a fix is implemented:

Your main problem is that nodes and labels overlap. As both are in a dark color, neither is clearly visible. However, the node layout actually seems to be pretty good, as it accentuates the hub-structure of the graph. So I would not change the edge length to space the nodes further apart.

In my opinion, your first option is to de-emphasize the nodes and edges, such that the labels become easier to read. This can be achieved by making the nodes and edges a lighter color.

Your second option is to offset the node labels from the nodes. However, this is non-trivial as you will want to prevent node label overlaps with other labels, other nodes, and the edges of the graph. Unfortunately, there isn't any functionality within networkx that reduces node label overlaps. However, to deal with this and other issues, I wrote netgraph, which is a network visualisation library and compatible with networkx graphs. My approach to avoiding node label overlaps is outlined here. However, if you tell netgraph to draw labels at a scalar offset, it will do just that, so there isn't anything special for you to do.

There's no simple built-in way, but you can achieve almost anything with the attributer like so:

Here is one solution. Since nodes that are identical strings, they will be assumed to be the same node by networkx. My solution was to just use integers for the nodes and apply node labels in the plot only via a dictionary mapping. I then calculated a custom dictionary of positions.

Also note that I renamed the graph to DG since this is the naming convention for directed graphs.

Unfortunately, the arrowheads look odd with matplotlib when plotting really thick lines, and according to this SO question I'm not sure that much can be done to fix it except manually adjusting some relevant parameters.

First the output, then the copy-pastable code:

You can align the nodes using a strong ("heavy") link, an invisible edge, between the last element of the first and the first element of the second node.

Add this line as the last one to your HTML-like code (which gives you much more flexibility than record shapes)