I found that base-pairs connections are not shown neither can I change the color of connections. It seems that when color is set to True variable "c" is set to "red" and that's it, while when color is set to False base-pairs connections are added to the plot. This PR should fix that and base-pairs connections should be visible now when color is set to True, and additionally it should support changing the color for base-pairs connections.
I found that base-pairs connections are not shown neither can I change the color of connections. It seems that when color is set to True variable "c" is set to "red" and that's it, while when color is set to False base-pairs connections are added to the plot. This PR should fix that and base-pairs connections should be visible now when color is set to True, and additionally it should support changing the color for base-pairs connections.