mne-tools / mne-tools/mne-python

Function _plot_connectivity_circle connects nodes with score zero

Open
#11,712 3 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

BUG
Dominant language
Python
Stars
3.5k
Forks
1.6k
Avg merge
1d 6h
Merged PRs (30d)
100

Description

Description of the problem

The function _plot_connectivity_circle shows links between nodes when the score between nodes is zero. One can observe this behavior when facecolor is set to a color different than black.

Steps to reproduce
import numpy as np
from mne.viz.circle import _plot_connectivity_circle
import matplotlib.pyplot as plt

A = np.array([[0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
              [0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
              [0.7, 0.5, 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
              [0.5, 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
              [0. , 0. , 0.8, 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
              [0.6, 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
              [0.8, 0. , 0.6, 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
              [0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ],
              [0. , 0. , 0. , 0. , 0. , 0.8, 0. , 0. , 0. , 0. ],
              [0. , 0. , 0. , 0.5, 0. , 0. , 0. , 0. , 0.6, 0. ]])

names = [f'X{i+1}' for i in range(A.shape[0])]

_plot_connectivity_circle(A, names, facecolor='white', textcolor='black',
                          node_edgecolor='white')
plt.show()
Expected results

I expect a figure that shows a link between a pair of nodes only when the score is large than zero. That's what one can observe when the function is used with the default values. The following is the figure I would expect:

image

Actual results

I get the following figure:

image

Additional information

It could be argued that this is not a bug. However, one can not observe links with zero scores when facecolor is set to black (default values).

Replacing

    ...
    # Finally, we draw the connections
    for pos, (i, j) in enumerate(zip(indices[0], indices[1])):
        t0, r0 = node_angles[i], 10

by

    # Finally, we draw the connections
    for pos, (i, j) in enumerate(zip(indices[0], indices[1])):
        if con_val_scaled[pos] == 0:
            continue
        # Start point
        t0, r0 = node_angles[i], 10

seems to solve the problem. I'll happily make a pull request if the main developers think it is useful.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start in mne.viz.circle at _plot_connectivity_circle and reproduce the issue with the provided matrix and facecolor='white'. Check how con_val_scaled and the connection loop handle zero values; done means the figure shows links only for positive scores while preserving the existing default behavior.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data-visualization
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
45/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.