fix: exclude confidence intervals of branches marked as bad
@@ -982,6 +982,7 @@ def plot_vs_years(tt, step = None, ax=None, confidence=None, ticks=True, **kwarg
raise NotReadyError("confidence needs to be either a float (for max posterior region) or a two numbers specifying lower and upper bounds")
for n in tt.tree.find_clades():
+ if not n.bad_branch:
pos = cfunc(n, confidence)
ax.plot(pos-offset, np.ones(len(pos))*n.ypos, lw=3, c=(0.5,0.5,0.5))
return fig, ax
