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When using plot_density on a 2D PCA projection of the well-known pentapeptide system, it looks to me as if variables are being plotted in reverse order in the density function (that is, $x$ and $y$ being swapped?) Unless I'm misunderstanding what it's supposed to be doing--it doesn't match the the output of plot_energy2d. I've attached my conda list so you can see the environment I'm working in (msmcondalist.txt).
Compare (pc2,pc1 in a different order in the two functions, result in plots that look the same):
fig,axes = plt.subplots(1,2,figsize=(8,3)) deeptime.plots.plot_density(pc1,pc2, ax=axes[0]) energies = deeptime.util.energy2d(pc2,pc1) deeptime.plots.plot_energy2d(energies,ax=axes[1]) for ax in axes.flat[1:]: ax.set_xlabel('PC 1') ax.set_ylabel('PC 2') fig.tight_layout()
which results in
versus (pc1,pc2 given in the same order in both functions)
fig,axes = plt.subplots(1,2,figsize=(8,3)) deeptime.plots.plot_density(pc1,pc2, ax=axes[0]) energies = deeptime.util.energy2d(pc1,pc2) deeptime.plots.plot_energy2d(energies,ax=axes[1]) for ax in axes.flat[1:]: ax.set_xlabel('PC 1') ax.set_ylabel('PC 2') fig.tight_layout()
which results in
The text was updated successfully, but these errors were encountered:
When using$x$ and $y$ being swapped?) Unless I'm misunderstanding what it's supposed to be doing--it doesn't match the the output of
plot_density
on a 2D PCA projection of the well-known pentapeptide system, it looks to me as if variables are being plotted in reverse order in the density function (that is,plot_energy2d
. I've attached my conda list so you can see the environment I'm working in (msmcondalist.txt).Compare (pc2,pc1 in a different order in the two functions, result in plots that look the same):
fig,axes = plt.subplots(1,2,figsize=(8,3))
deeptime.plots.plot_density(pc1,pc2, ax=axes[0])
energies = deeptime.util.energy2d(pc2,pc1)
deeptime.plots.plot_energy2d(energies,ax=axes[1])
for ax in axes.flat[1:]:
ax.set_xlabel('PC 1')
ax.set_ylabel('PC 2')
fig.tight_layout()
which results in
versus (pc1,pc2 given in the same order in both functions)
fig,axes = plt.subplots(1,2,figsize=(8,3))
deeptime.plots.plot_density(pc1,pc2, ax=axes[0])
energies = deeptime.util.energy2d(pc1,pc2)
deeptime.plots.plot_energy2d(energies,ax=axes[1])
for ax in axes.flat[1:]:
ax.set_xlabel('PC 1')
ax.set_ylabel('PC 2')
fig.tight_layout()
which results in
The text was updated successfully, but these errors were encountered: