Graph plotting: vertex colors

[jmantysalo]

This is a first part of #13827.

Currently setting a color for one vertex will change default pink to blue in other vertices. This patch will correct it. Also we make it possible to set a default color with vertex_color and have some vertices colored differently with vertex_colors. To test try for example

sage: g=graphs.PetersenGraph()
sage: g.show()
sage: g.show(vertex_color='green')
sage: g.show(vertex_colors={'red': [0,1], 'blue': [3,4]})
sage: g.show(vertex_color='green', vertex_colors={'red': [0,1], 'blue': [3,4]})
sage: g.show(vertex_colors='green')

[jmantysalo]

On a way to more customizable graph plotting.

---

New commits:

​b8e8b5c

Modified setting of graph vertices colors.

[paulmasson]

Doctests pass. Documentation builds. Example runs as expected.

It looks like you took out some default rainbow coloring in the code. Since this is a part of Sage I'm unlikely to use much, I would like to understand the impact this will have on other users. While it's certainly better to have more control over the coloring, how many people are likely to complain if the rainbow coloring is gone?

[jmantysalo]

Replying to paulmasson:

It looks like you took out some default rainbow coloring in the code.

I was not able to run that part of code. It seems to refer partition-option. However, currently

g = graphs.PetersenGraph()
g.show(partition=[[1,2],[3,4]])

have same problem of changing default color for non-listed vertices. With this patch they will stay pink, and also you can say

g.show(partition=[[1,2],[3,4]], vertex_color='gray')

[jmantysalo]

Sidenote, there was also a plain error in documentation: "If a vertex is not listed, it looks invisible on the resulting plot (it does not get drawn)." was not true, and is not after this patch.

[paulmasson]

The current code doesn't appear to have a default color. Nonlisted vertices are given a random color, not a default color. This ticket modifies that behavior.

If that is a good idea then I'm fine with it, but I would rather have some additional input. Nathann Cohen wrote the original coloring code in 2009, so I'd like to hear from him or interested others on this change.

[jmantysalo]

Replying to paulmasson:

The current code doesn't appear to have a default color. Nonlisted vertices are given a random color, not a default color.

Kind of, but always same color. Setting a color of one vertex to blue or green make others red, setting a color to red make others light blue etc.

If that is a good idea then I'm fine with it, but I would rather have some additional input. Nathann Cohen wrote the original coloring code in 2009, so I'd like to hear from him or interested others on this change.

Me too, but Nathann faded from developers some time ago. :=( See for example ​https://groups.google.com/forum/#!topic/sage-devel/-Z5kXJv6ZQA

[paulmasson]

Jori, I started reading sage-devel some time after that thread, so thanks for sharing. I've seen some other comments since then about the same topic but didn't realize it was such an issue. I've removed him from this ticket.

I'd like to wait a couple days to see if Karl-Dieter or Travis want to chime in. If we don't hear from them soon then I'll set positive review. I certainly don't want to deter an active developer!

[tscrim]

I don't have a real preference for this because I never really use it. If you want additional input, you're probably best posting to sage-devel.

[vbraun]

sage -t --long src/sage/combinat/words/finite_word.py
**********************************************************************
File "src/sage/combinat/words/finite_word.py", line 116, in sage.combinat.words.finite_word
Failed example:
    st.show(word_labels=True)
Expected nothing
Got:
    doctest:270: DeprecationWarning: Use of vertex_colors=<string> is deprecated, use vertex_color=<string> and/or vertex_colors=<dict>.
    See http://trac.sagemath.org/21048 for details.
**********************************************************************
1 item had failures:
   1 of  56 in sage.combinat.words.finite_word
    [1244 tests, 1 failure, 11.63 s]
sage -t --long src/sage/combinat/words/suffix_trees.py
**********************************************************************
File "src/sage/combinat/words/suffix_trees.py", line 867, in sage.combinat.words.suffix_trees.ImplicitSuffixTree.?
Failed example:
    ImplicitSuffixTree(Word('cacao')).plot(word_labels=True)
Expected:
    Graphics object consisting of 23 graphics primitives
Got:
    doctest:270: DeprecationWarning: Use of vertex_colors=<string> is deprecated, use vertex_color=<string> and/or vertex_colors=<dict>.
    See http://trac.sagemath.org/21048 for details.
    Graphics object consisting of 23 graphics primitives
**********************************************************************
1 item had failures:
   1 of   7 in sage.combinat.words.suffix_trees.ImplicitSuffixTree.?
    [245 tests, 1 failure, 3.03 s]

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​60b487d

Corrections to words.

[jmantysalo]

Badly corrected, but at least works. I guess words- and posets-directories should be checked when graph plotting is ready.

[paulmasson]

vertex_colors is defined as a dicitionary in suffix_trees.py as it should be, so the changes you made aren't the best. The problem is the misspelling veretex_colors on line 885. Please revert the changes you just made and correct that spelling. I've already tested this and it solves both doctest failures.

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​2e59975

Revert "Corrections to words."

[git]

Branch pushed to git repo; I updated commit sha1. New commits:

​34be2bb

Typo on variable name corrected.

[jmantysalo]

I was blind.

[paulmasson]

All doctests pass in combinat/words and combinat/posets