The axis labels are text objects with the same properties. (Although not all the properties, such as 'VerticalAlignment' are listed in the ylabel properties, they can still be adressed.)
Try this —
hold on
scatter(-rand(1,10),rand(1,10),120,'or','filled')
scatter(rand(1,10),rand(1,10),120,'ob','filled')
ax = gca;
ax.YAxisLocation = 'origin';
hyl = ylabel('my y-label');
% get(hyl)
pos = hyl.Position;
hyl.Position(2) = mean(ylim); % Use Original Values, Excep[t For The 'y' Coordinate
hyl.Rotation = 90; % Change 'Rotation' Value
hyl.VerticalAlignment = 'middle'; % Set Hidden 'text' Property
There are still other tweaks possible if this is not exactly what you want.
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