I’m creating some plots with histograms and a color bar, but I’m struggling with the huge white gaps between subplots and I don’t know how to reduce them. This an example of a more complex code:
import numpy as np
import matplotlib.pyplot as plt
ihist = np.array([
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
])
vhist = np.array([
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
])
mins = [1014.3484983803353, -168.92777938399416]
maxs = [5420.578637599565, 1229.7294914536292]
labels = ['x ($\AA$)', 'y ($\AA$)']
fig = plt.figure()
# SIAs
iax = plt.subplot2grid((9, 2), (1, 0), rowspan=8)
iax.set_xlabel(labels[0])
iax.set_xlim(mins[0], maxs[0])
iax.set_ylabel(labels[1])
iax.set_ylim(mins[1], maxs[1])
iax.imshow(ihist, origin="lower", extent=[mins[0], maxs[0], mins[1], maxs[1]])
# Vacancies
vax = plt.subplot2grid((9, 2), (1, 1), rowspan=8)
vax.set_xlabel(labels[0])
vax.set_xlim(mins[0], maxs[0])
vax.set_ylabel(labels[1])
vax.set_ylim(mins[1], maxs[1])
vax.yaxis.set_label_position("right")
vax.yaxis.tick_right()
vax_img = vax.imshow(vhist, origin="lower", extent=[mins[0], maxs[0], mins[1], maxs[1]])
# Color bar
cax = plt.subplot2grid((9, 2), (0, 0), colspan=2)
cbar = fig.colorbar(vax_img, cax=cax, orientation="horizontal")
cbar.set_label("Counts per ion")
cbar.ax.xaxis.set_ticks_position("top")
cbar.ax.xaxis.set_label_position("top")
plt.tight_layout()
plt.show()
And this is the output:
as you can see there are unnecessary white spaces between the color bar and the histograms, and between the histograms and the bottom of the figure. I want to remove them.
I think they are caused by things like plt.subplot2grid((9, 2), (1, 0), rowspan=8) but I did it that way to reduce the vertical size of the color bar.
Note: in the real code, limits are obtained on the fly, so histograms might have same hight and width or not.
This is due to the aspect ratio setting of imshow. If you use:
...
iax.imshow(ihist, origin="lower", extent=[mins[0], maxs[0], mins[1], maxs[1]], aspect="auto")
...
vax_img = vax.imshow(vhist, origin="lower", extent=[mins[0], maxs[0], mins[1], maxs[1]], aspect="auto")
i.e., add aspect="auto", to your imshow calls, it should look as you expect. Note that you may want to switch to using add_gridspec and add_subplot, to allow finer degrees of control over the grid. E.g., an equivalent would be:
...
fig = plt.figure()
# SIAs
# add a two by two grid using the required height ratios
gs = fig.add_gridspec(
2, 2, height_ratios=(1, 9)
)
iax = fig.add_subplot(gs[1, 0])
iax.set_xlabel(labels[0])
iax.set_xlim(mins[0], maxs[0])
iax.set_ylabel(labels[1])
iax.set_ylim(mins[1], maxs[1])
iax.imshow(ihist, origin="lower", extent=[mins[0], maxs[0], mins[1], maxs[1]], aspect="auto")
# Vacancies
vax = fig.add_subplot(gs[1, 1])
vax.set_xlabel(labels[0])
vax.set_xlim(mins[0], maxs[0])
vax.set_ylabel(labels[1])
vax.set_ylim(mins[1], maxs[1])
vax.yaxis.set_label_position("right")
vax.yaxis.tick_right()
vax_img = vax.imshow(vhist, origin="lower", extent=[mins[0], maxs[0], mins[1], maxs[1]], aspect="auto")
# Color bar
cax = fig.add_subplot(gs[0, :])
cbar = fig.colorbar(vax_img, cax=cax, orientation="horizontal")
cbar.set_label("Counts per ion")
cbar.ax.xaxis.set_ticks_position("top")
cbar.ax.xaxis.set_label_position("top")
# also try constrained layout rather than tight layout
fig.set_layout_engine("constrained")
plt.show()
Suggest using layout='compressed', setting at the beginning, and using the fact that colorbars can be added directly with fig.colorbar(im, ax=axs, location='top'):
There will still be substantial white space because of the aspect ratio of your axes, but the white space will be on the outside of the figure where it is easy to trim, rather than between your colorbar and your axes. Note that if you want to trim this space, it is possible to use fig.savefig('name.png', bbox_inches='tight')
import numpy as np
import matplotlib.pyplot as plt
...
mins = [1014.3484983803353, -168.92777938399416]
maxs = [5420.578637599565, 1229.7294914536292]
labels = ['x ($\AA$)', 'y ($\AA$)']
fig, axs = plt.subplots(1, 2, layout='compressed')
iax = axs[0]
vax = axs[1]
iax.set_xlabel(labels[0])
iax.set_xlim(mins[0], maxs[0])
iax.set_ylabel(labels[1])
iax.set_ylim(mins[1], maxs[1])
iax.imshow(ihist, origin="lower", extent=[mins[0], maxs[0], mins[1], maxs[1]])
# Vacancies
vax.set_xlabel(labels[0])
vax.set_xlim(mins[0], maxs[0])
vax.set_ylabel(labels[1])
vax.set_ylim(mins[1], maxs[1])
vax.yaxis.set_label_position("right")
vax.yaxis.tick_right()
vax_img = vax.imshow(vhist, origin="lower", extent=[mins[0], maxs[0], mins[1], maxs[1]])
# Color bar
cbar = fig.colorbar(vax_img, ax=axs, location="top")
cbar.set_label("Counts per ion")
plt.show()