Add legend to scatter plot (PCA)
I recently proposed an easy way to add a legend to a scatter, see GitHub PR. This is still being discussed.
In the meantime you need to manually create your legend from the unique labels in y. For each of them you'd create a Line2D object with the same marker as is used in the scatter plot and supply them as argument to plt.legend.
scatter = plt.scatter(xs * scalex,ys * scaley, c = y)
labels = np.unique(y)
handles = [plt.Line2D([],[],marker="o", ls="",
color=scatter.cmap(scatter.norm(yi))) for yi in labels]
plt.legend(handles, labels)
