Common xlabel/ylabel for matplotlib subplots

Question

This looks like what you actually want. It applies the same approach of this answer to your specific case:

import matplotlib.pyplot as plt

fig, ax = plt.subplots(nrows=3, ncols=3, sharex=True, sharey=True, figsize=(6, 6))

fig.text(0.5, 0.04, 'common X', ha='center')
fig.text(0.04, 0.5, 'common Y', va='center', rotation='vertical')

Since I consider it relevant and elegant enough (no need to specify coordinates to place text), I copy (with a slight adaptation) an answer to another related question.

import matplotlib.pyplot as plt
fig, axes = plt.subplots(5, 2, sharex=True, sharey=True, figsize=(6,15))
# add a big axis, hide frame
fig.add_subplot(111, frameon=False)
# hide tick and tick label of the big axis
plt.tick_params(labelcolor='none', which='both', top=False, bottom=False, left=False, right=False)
plt.xlabel("common X")
plt.ylabel("common Y")

This results in the following (with matplotlib version 2.2.0):

New in Matplotlib v3.4 (pip install matplotlib --upgrade)

supxlabel and supylabel

    fig.supxlabel('common_x')
    fig.supylabel('common_y')

See example:

import matplotlib.pyplot as plt

for tl, cl in zip([True, False, False], [False, False, True]):
    fig = plt.figure(constrained_layout=cl, tight_layout=tl)

    gs = fig.add_gridspec(2, 3)

    ax = dict()

    ax['A'] = fig.add_subplot(gs[0, 0:2])
    ax['B'] = fig.add_subplot(gs[1, 0:2])
    ax['C'] = fig.add_subplot(gs[:, 2])

    ax['C'].set_xlabel('Booger')
    ax['B'].set_xlabel('Booger')
    ax['A'].set_ylabel('Booger Y')
    fig.suptitle(f'TEST: tight_layout={tl} constrained_layout={cl}')
    fig.supxlabel('XLAgg')
    fig.supylabel('YLAgg')
    
    plt.show()

see more

Without sharex=True, sharey=True you get:

With it you should get it nicer:

fig, axes2d = plt.subplots(nrows=3, ncols=3,
                           sharex=True, sharey=True,
                           figsize=(6,6))

for i, row in enumerate(axes2d):
    for j, cell in enumerate(row):
        cell.imshow(np.random.rand(32,32))

plt.tight_layout()

But if you want to add additional labels, you should add them only to the edge plots:

fig, axes2d = plt.subplots(nrows=3, ncols=3,
                           sharex=True, sharey=True,
                           figsize=(6,6))

for i, row in enumerate(axes2d):
    for j, cell in enumerate(row):
        cell.imshow(np.random.rand(32,32))
        if i == len(axes2d) - 1:
            cell.set_xlabel("noise column: {0:d}".format(j + 1))
        if j == 0:
            cell.set_ylabel("noise row: {0:d}".format(i + 1))

plt.tight_layout()

Adding label for each plot would spoil it (maybe there is a way to automatically detect repeated labels, but I am not aware of one).

Since the command:

fig,ax = plt.subplots(5,2,sharex=True,sharey=True,figsize=fig_size)

you used returns a tuple consisting of the figure and a list of the axes instances, it is already sufficient to do something like (mind that I've changed fig,axto fig,axes):

fig,axes = plt.subplots(5,2,sharex=True,sharey=True,figsize=fig_size)

for ax in axes:
    ax.set_xlabel('Common x-label')
    ax.set_ylabel('Common y-label')

If you happen to want to change some details on a specific subplot, you can access it via axes[i] where i iterates over your subplots.

It might also be very helpful to include a

fig.tight_layout()

at the end of the file, before the plt.show(), in order to avoid overlapping labels.

It will look better if you reserve space for the common labels by making invisible labels for the subplot in the bottom left corner. It is also good to pass in the fontsize from rcParams. This way, the common labels will change size with your rc setup, and the axes will also be adjusted to leave space for the common labels.

fig_size = [8, 6]
fig, ax = plt.subplots(5, 2, sharex=True, sharey=True, figsize=fig_size)
# Reserve space for axis labels
ax[-1, 0].set_xlabel('.', color=(0, 0, 0, 0))
ax[-1, 0].set_ylabel('.', color=(0, 0, 0, 0))
# Make common axis labels
fig.text(0.5, 0.04, 'common X', va='center', ha='center', fontsize=rcParams['axes.labelsize'])
fig.text(0.04, 0.5, 'common Y', va='center', ha='center', rotation='vertical', fontsize=rcParams['axes.labelsize'])