Edge length?

[jordansaethre]

Is there a way to dictate how long the edges are based on the nodes that are being connected? I have been using this tool to visualize a simplicial complex that is the result of my own algorithm (not the mapper algorithm) and I want edge length to have meaning. If this is not already a feature would anyone be able to point me to the section of code that I would need to modify to make this happen? I have messed around with quite a few things, but haven't had any luck.

[deargle]

The underlying library for the html vis is d3 force graph, and no, you can't specify edge length.

…

On Mon, Sep 14, 2020, 8:04 AM jordansaethre ***@***.***> wrote: Is there a way to dictate how long the edges are based on the nodes that are being connected? I have been using this tool to visualize a simplicial complex that is the result of my own algorithm (not the mapper algorithm) and I want edge length to have meaning. If this is not already a feature would anyone be able to point me to the section of code that I would need to modify to make this happen? I have messed around with quite a few things, but haven't had any luck. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#197>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAI6Y7O4LNYNR7XY5OFRJR3SFYPINANCNFSM4RLUSCSQ> .

[sauln]

If you're okay with static graphs, the plotly visualization functionality should let you specify edge lengths. The entry point is here:

kepler-mapper/kmapper/plotlyviz.py

Lines 61 to 86 in 956b8c9

	def plotlyviz(
	scomplex,
	colorscale=None,
	title="Kepler Mapper",
	graph_layout="kk",
	color_values=None,
	color_function_name=None,
	dashboard=False,
	graph_data=False,
	factor_size=3,
	edge_linewidth=1.5,
	node_linecolor="rgb(200,200,200)",
	width=600,
	height=500,
	bgcolor="rgba(240, 240, 240, 0.95)",
	left=10,
	bottom=35,
	summary_height=300,
	summary_width=600,
	summary_left=20,
	summary_right=20,
	hist_left=25,
	hist_right=25,
	member_textbox_width=800,
	filename=None,
	):

Right now, it does not support supplying some sort of distance matrix, but I believe you should be able to thread a parameter all the way down to the point the graph_layout argument is used.

You might also try the networkx visualizations. They could be easier to work with.

[deargle]

In addition to @sauln 's, suggestions, I also misspoke -- d3 force graphs do let you specify link distance, see https://github.com/d3/d3-force#link_distance . I have a PR in the works that upgrades d3 to the latest version which use the linked docs

[sauln]

It might be possible to overwrite the d3 force layout also..

kepler-mapper/kmapper/static/kmapper.js

Lines 127 to 131 in 956b8c9

	var force = d3.layout.force()
	.linkDistance(5)
	.gravity(0.2)
	.charge(-1200)
	.size([w,h]);

You can supply a function to the linkDistance method that will instantiate the distance for each link. For an example, you can see http://bl.ocks.org/sathomas/83515b77c2764837aac2

force.linkDistance(function(link) {
  return link.graph === 0 ? height/2 : height/4;
});

Maybe instead you could do something like

force.linkDistance(function(link) {
  return link.length;
});

and then turn gravity (and probably other parameters) to 0 so the link length doesn't change?

[sauln]

@jordansaethre If you can get it to work, it'd be awesome to have this as a contribution to the library!

[deargle]

@sauln I think the more recent versions of d3-force respect the link distance more than the current version does, so gravity wouldn't have to be messed with. Also, I think the concept of gravity has been replaced by charge in the latest versions. You can see some of the changes I had to make to the force layout in the most recent wip pr.

[deargle]

To emphasize, if any work is going to be done on this, the changes between the d3-force version used in my WIP and the version on master are so drastic, that any changes to the d3 code should hold off a bit.

See 79ec3bd

[jordansaethre]

@sauln @deargle I will definitely give it a shot. Thanks for the tips guys!