graph plotting -- ploting of graphs (networks) is somehow messed up/scaled wrong/cropped wrong since it doesn't work with graphics_array

[williamstein]

Want to see some truly hideous plotting output? Try this:

Q = GraphQuery(display_cols=['graph6','num_vertices','degree_sequence'],num_edges=['<=',5],min_degree=1)

v = Q.get_graphs_list(); v

graphics_array([g.plot() for g in v], 3, len(v)//3).show()

I guess the problem is maybe Networkx drawing the plots instead of Sage (??), hence the cropping/layout is wrong? I don't know. Why do we use networkx at all for any part of plotting? It would be better to plot to native Sage primitives, wouldn't it?

Fixed by #9211.

Component: graph theory

Reviewer: Jason Grout

Issue created by migration from https://trac.sagemath.org/ticket/5938

[williamstein]

comment:1

Even this (following the above example), results in hideous mis-cropped plots, and it doesn't use graphics array at all:

for g in v[:5]:
    show(g,figsize=2)

[williamstein]

comment:2

And even this results in bits being chopped off that shouldn't be!

for g in v[:5]:
    show(g)

[sagetrac-ekirkman]

comment:3

I'm still working on this, but I have some updates. It looks like the first problem is the buffer size on scatter_plot. It's including the points, but not the vertex radius of the outermost points. That should be simple enough to fix, but then I'll also look at some auto-scaling to make the graphics_array a little nicer. I also feel like the graphs_list module had some nice parameters for graphics_arrays of graphs, but they might be outdated now that graph plotting is native in Sage. I'll check into that too though.

[jasongrout]

comment:4

See http://groups.google.com/group/sage-support/browse_thread/thread/274d540f783603e7/e43c031f36672d85

[williamstein]

comment:5

THIS SUCKS!!!!!!!!!!!

I can't believe how annoying it is that plotting graphs is still so totally and completely broken. It is really, really horrible. I don't know how anybody can stand this.

Frickin' a. Every single graph plot I try has the borders chopped off. E.g.,

sage: Q = GraphQuery(display_cols=['graph6','num_vertices','degree_sequence'], num_edges=['<=',5],min_degree=1)
sage: Q.show(with_picture=True)
[[hideous pain]]

[rlmill]

comment:6

Fix it!

[rlmill]

comment:7

Warning- I've seen several "fixes" for this go in, and yet it's still borken

[jasongrout]

comment:8

See #9211 for progress towards a fix.

[jasongrout]

comment:9

Graph vertices are not cut off anymore. The plot in the description has overlapping vertices, though.

[jasongrout]

comment:10

This is a dup of #9211. Since the patch is there, and it is already merged, I'm calling this the duplicate.

[jdemeyer]

Reviewer: Jason Grout