# Creating subplots with plot\_connectivity\_circle

**URL:** <https://mne.discourse.group/t/creating-subplots-with-plot-connectivity-circle/7359>\
**Category:** Support & Discussions\
**Tags:** visualization\
**Created:** [August 10, 2023, 7:55pm UTC](https://mne.discourse.group/t/creating-subplots-with-plot-connectivity-circle/7359 "2023-08-10T19:55:27Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![cwilliams](https://avatars.discourse-cdn.com/v4/letter/c/ecccb3/32.png) [@cwilliams](https://mne.discourse.group/u/cwilliams)\
**Post date:** [August 10, 2023, 7:55pm UTC](https://mne.discourse.group/t/creating-subplots-with-plot-connectivity-circle/7359/1 "2023-08-10T19:55:27Z")

</div>

Hey everyone,

I am trying to create a 3-part plot with **mne\_connectivity.viz.plot\_connectivity\_circle** using **coherence** data that I have already processed\*\* - where each subplot would visualize coherence at a different frequency band. So to begin with, I am having trouble with the example [here](https://mne.tools/mne-connectivity/stable/auto_examples/mne_inverse_label_connectivity.html) which uses the following:

```python
fig, axes = plt.subplots(1, 3, figsize=(8, 4), facecolor='black',
                         subplot_kw=dict(polar=True))
no_names = [''] * len(label_names)
for ax, method in zip(axes, con_methods):
    plot_connectivity_circle(con_res[method], no_names, n_lines=300,
                             node_angles=node_angles, node_colors=label_colors,
                             title=method, padding=0, fontsize_colorbar=6,
                             ax=ax)

```

In the example, the 3-part subplot calls on a dict object “con\_res.” However this is a collection of 3 arrays collected from some other dataset using 3 methods (I really don’t understand what they’re doing to create it here):

```python
con_methods = ['pli', 'wpli2_debiased', 'ciplv']
con = spectral_connectivity_epochs(
    label_ts, method=con_methods, mode='multitaper', sfreq=sfreq, fmin=fmin,
    fmax=fmax, faverage=True, mt_adaptive=True, n_jobs=1)

# con is a 3D array, get the connectivity for the first (and only) freq. band
# for each method
con_res = dict()
for method, c in zip(con_methods, con):
    con_res[method] = c.get_data(output='dense')[:, :, 0]

```

So essentially, I want to manually create a dict that contains 3 different arrays that can be called on in the function similar to how they do with (con\_res[method],…).

If I replace the dict with a single array (theta, for instance), the code “works” and returns 1 subplot + 2 blank ones. But if I try to add my 3 arrays into a dict manually and then call on it, I recieve the following error:

```python

  File ~\AppData\Local\mne-python\1.4.2_0\lib\site-packages\mne\viz\circle.py:198 in _plot_connectivity_circle
    if con.ndim == 1:

AttributeError: 'dict' object has no attribute 'ndim'

```

Here is what I have tried:

```python
import numpy as np
import matplotlib.pyplot as plt
import mne
from mne.viz import circular_layout
from mne_connectivity.viz import plot_connectivity_circle
import pandas as pd
    
#excel matrices each with coherence in a single frequency band
dft = pd.read_excel("Theta_Differences.xlsx")
theta=dft.to_numpy()

dfb = pd.read_excel("Beta_Differences.xlsx")
beta=dfb.to_numpy()

dflg = pd.read_excel("Low_Gamma_Differences.xlsx")
low_gamma=dflg.to_numpy()

#Here I try to create a dict containing the 3 arrays
con_bands={"Theta":theta,"beta":beta,"Low Gamma":low_gamma}

#A list of the 8 recorded regions
node_order= ["rACC", "PrL", "cACC", "CA1", "mEC", "OFC", "aPCx", "pPPx"]
label_names = ["rACC", "PrL", "cACC", "CA1", "mEC", "OFC", "aPCx", "pPPx"]
node_angles = circular_layout(label_names, node_order, start_pos=90)

###########################
#Single circle graph (works)
fig, ax = plt.subplots(figsize=(8, 8), facecolor='black',
                       subplot_kw=dict(polar=True))
plot_connectivity_circle(theta, label_names, n_lines=28, node_angles=node_angles, title="Change in Coherence from Baseline (Theta)" )
fig.tight_layout()

#################
##Subplot (Error)

fig, axes = plt.subplots(1, 3, figsize=(8, 4), facecolor='black',
                         subplot_kw=dict(polar=True))
no_names = [''] * len(label_names)
for ax, method in zip(axes, con_bands):
    plot_connectivity_circle(con_bands, no_names, n_lines=28, node_angles=node_angles, padding=0, fontsize_colorbar=6,
                             ax=ax )

```

I realize this is an embarrassingly bad attempt. But I have pretty much zero python experience, so I’m really just trying one thing after another to see if I can get something to happen. For anyone with time to waste, I am also on discord! Thank you!

---

<div class="post-metadata">

**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\
**Post date:** [August 10, 2023, 10:41pm UTC](https://mne.discourse.group/t/creating-subplots-with-plot-connectivity-circle/7359/2 "2023-08-10T22:41:39Z")

</div>

> [@cwilliams](#):
>
> However this is a collection of 3 arrays collected from some other dataset using 3 methods (I really don’t understand what they’re doing to create it here):

The function `spectral_connectivity_epochs` allows you to compute connectivity using multiple different methods all at once (because this is more efficient than making 3 separate function calls for the 3 methods).

So `con_res` here basically just splits the output of `spectral_connectivity_epochs` by putting each of the different method names as keys, and the different method results as values.

I think what’s missing from your attempt is in the for-loop that calls `plot_connectivity_circle` you need to pass `con_bands[method]` rather than just `con_bands`. And while you’re at it, change the looping variable name from `method` to `band` (to reflect what you’re doing):

```python
for ax, band in zip(axes, con_bands):
    plot_connectivity_circle(con_bands[band], no_names, n_lines=28, node_angles=node_angles, padding=0, fontsize_colorbar=6,
                             ax=ax )

```

---

<div class="post-metadata">

**Author:** ![cwilliams](https://avatars.discourse-cdn.com/v4/letter/c/ecccb3/32.png) [@cwilliams](https://mne.discourse.group/u/cwilliams)\
**Post date:** [August 10, 2023, 10:56pm UTC](https://mne.discourse.group/t/creating-subplots-with-plot-connectivity-circle/7359/3 "2023-08-10T22:56:05Z")

</div>

> [@drammock](#):
>
> I think what’s missing from your attempt is in the for-loop that calls `plot_connectivity_circle` you need to pass `con_bands[method]` rather than just `con_bands`. And while you’re at it, change the looping variable name from `method` to `band` (to reflect what you’re doing):

Thanks so much for the reply! I really appreciate your time!

So oddly enough, I actually tried this! And when I do, I get the first plot. But the second and third are missing. Initially I thought I must’ve had the con\_bands[band] part wrong. But I went back and tried running the example with the sample data - and it also is no longer drawing the second or third plots! I receive 1 completed circle graph along with 2 blank circle graphs.

Is something wrong with my MNE library?

I was thinking it may be the library. So I went home and tried it on another PC, and I’m getting the same problem. I receive no errors, so it’s a real head-scratcher

Edit: I’m not sure why, but saving the plot directly to file actually shows all of the plots. It just won’t show up in the plots frame in Spyder (Saving from the plots frame also doesn’t work).

---

<div class="post-metadata">

**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\
**Post date:** [August 11, 2023, 1:38am UTC](https://mne.discourse.group/t/creating-subplots-with-plot-connectivity-circle/7359/4 "2023-08-11T01:38:23Z")

</div>

Try adding this to the top of your script:

```python
import matplotlib.pyplot as plt
plt.ion()

```

that might fix it.

---

<div class="post-metadata">

**Author:** ![cwilliams](https://avatars.discourse-cdn.com/v4/letter/c/ecccb3/32.png) [@cwilliams](https://mne.discourse.group/u/cwilliams)\
**Post date:** [August 11, 2023, 2:05am UTC](https://mne.discourse.group/t/creating-subplots-with-plot-connectivity-circle/7359/5 "2023-08-11T02:05:07Z")

</div>

No affect, unfortunately.

For now, I’m at least able to output a few figures (which, honestly, I thought would take me months - not days. So I’m still pretty stoked to get anything).

When I get back to it tomorrow, I’m trying to see if I can change the color of the scale/lines so I can reflect negative numbers (even if it’s not necessarily conventional).

(I feel like you deserve to see them since you helped haha)  
 ![All Frequencies](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/d/dd923da0ca03e7f479c3e46f33da1c4c783837ca.png)  
 ![Low Gamma](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/a/ae88ee73ce243f1640e7d2908df8eb9c1720857c.png)  
 ![Theta](https://global.discourse-cdn.com/free1/uploads/mne/original/2X/1/1dd5199f48a9bda8428c2091b2e147dcd144d995.png)

---

<div class="post-metadata">

**Author:** ![drammock](https://yyz2.discourse-cdn.com/free1/user_avatar/mne.discourse.group/drammock/32/4_2.png) [@drammock](https://mne.discourse.group/u/drammock)\
**Post date:** [August 11, 2023, 6:25am UTC](https://mne.discourse.group/t/creating-subplots-with-plot-connectivity-circle/7359/6 "2023-08-11T06:25:59Z")

</div>

not sure what’s going wrong; this works for me (yields a figure with 3 circular plots):

```python
import matplotlib.pyplot as plt
import numpy as np
from mne_connectivity.viz import plot_connectivity_circle

rng = np.random.default_rng(seed=73)
plt.ion()

bands = dict(
    alpha=rng.uniform(size=(10, 10)),
    beta=rng.uniform(size=(10, 10)),
    gamma=rng.uniform(size=(10, 10)),
)
node_names = list('abcdefghij')

fig, axs = plt.subplots(1, 3, facecolor='k', subplot_kw=dict(polar=True))

for ax, band in zip(axs, bands):
    plot_connectivity_circle(bands[band], node_names=node_names, title=band, ax=ax)

```

_EDIT:_ I just saw that you mentioned the Spyder plots pane. I’ll guess that this is the problem. Embedded plot panes in IDEs like Spyder or PyCharm often do funny/custom things to “intercept” matplotlib plots and display them where they want them; unfortunately side effects like this are not uncommon.