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Function _plot_connectivity_circle connects nodes with score zero #11712

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aweinstein opened this issue May 29, 2023 · 3 comments · May be fixed by #12210
Open

Function _plot_connectivity_circle connects nodes with score zero #11712

aweinstein opened this issue May 29, 2023 · 3 comments · May be fixed by #12210
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@aweinstein
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aweinstein commented May 29, 2023 •
edited

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.
@aweinstein aweinstein added the BUG label May 29, 2023
@drammock
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sorry for the slow reply! Your proposed fix looks reasonable. Still willing to open a PR?

@aweinstein
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Sure! I'll do it next week.

@aweinstein aweinstein linked a pull request Nov 15, 2023 that will close this issue
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@aweinstein
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Sorry for the delay. I just submitted pull request #12210.

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@aweinstein @drammock