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as you can see I have shifted up the second axis. However I would like to fix the zero as it has been disconnected from the y axis.

enter image description here


date coordinates in=x,
width=12cm,height=5.5cm, scale only axis,
xticklabel style={align=center, rotate=90, anchor=near xticklabel},
major x tick style = transparent,

anchor=north west,
width=12cm,height=1.5cm, scale only axis,major x tick style = transparent,
minor x tick num = 0,

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I suspect that you need to fix at least the lower y limit of the second axis, i.e. to add ymin=0 to your axis.

If your axes are both empty, you may see a warning claiming that

! Package pgfplots Warning: You have an axis with empty range. Replacing it with a default range and clearing all plots.

in this case, you have to provide all limits of the affected axis manually.

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