The following code shows my problem. plotyy completely fails if the ticks are not at the same positions on both sides (which is rather the normal case…)
I require a plot with two y axis but the ticks only on one side. I was suggested to use addaxis, but I do not see how that helps me, since I do not want separated axis.
clf;
clc;
xaxis = 0:0.1:25;
ydata1 = linspace(12.1712,12.7679, length(xaxis));
ydata2 = linspace(0.3597,-28.7745, length(xaxis));
[AX,H1,H2] = plotyy(xaxis, ydata1, xaxis, ydata2);
% axis limits - x axis (min to max)
xlimits(1) = min(xaxis); xlimits(2) = max(xaxis);
set(AX, 'XLim', xlimits);
set(AX(2),'XTick',[]);
% y1 axis limits
ylimits(1) = min(ydata1); ylimits(2) = max(ydata1);
ylimits(2) = ylimits(2) + (ylimits(2)-ylimits(1))*0.05;
set(AX(1), 'YLim', ylimits);
% y2 axis limits
ylimits(1) = min(ydata2); ylimits(2) = max(ydata2);
ylimits(2) = ylimits(2) + (ylimits(2)-ylimits(1))*0.05;
set(AX(2), 'YLim', ylimits);
% y1 ticks
set(AX(1),'YTick',[12.0:0.1:12.8]);
% y2 ticks
set(AX(2),'YTick',[-25:5:0]);
print(gcf, ['-r' num2str(400)], ['test' '.png' ], ['-d' 'png']);

Here is an approach that I got from the mathworks forum. The idea is to remove the box property, which creates the tics on the opposite side.
The downside is, that the upper line disappears. If someone knows how to get it back that would be great. Mybe with an empty plot over the current plot with the same dimensions??