Question

I’m producing a double panel figure in Mathematica. The Bottom panel has negative values on the y-axis and this causes the label on that axis, produced using FrameLabel, to be aligned a bit more to the left than the label on the top panel, which has positive values. I cannot join the panels to a single plot because the scales are different.
A piece of code that reproduces the problem:

pad = 80;
Export["C:\\Users\\user\\Desktop\\stackoverflow.png",
 Column[
  {
   Show[
    Plot[ Sin[x]^2, {x, 0, Pi},
     FrameLabel -> {"", "y"},
     BaseStyle -> {FontSize -> 16, FontWeight -> Bold, 
       FontFamily -> "Calibri"},
     ImagePadding -> {{pad, pad/4}, {pad, pad/4}},
     Frame -> {True, True, True, True}
     ]
    , ImageSize -> 640]
   ,
   Show[
    Plot[ -Sin[x]^2/1000, {x, 0, Pi},
     FrameLabel -> {"x", "y"},
      BaseStyle -> {FontSize -> 16, FontWeight -> Bold, 
       FontFamily -> "Calibri"},
     ImagePadding -> {{pad, pad/4}, {pad, pad/4}},
     Frame -> {True, True, True, True}
     ]
    , ImageSize -> 640]
   }
  ]
 ]

This code produces the following figure, in which you can see that the y label is aligned differentyl in the top and bottom panels.

I would appreciate any help – I have to submit the figure (obviously no the above figure…) to the publisher ASAP for my paper to go to print…
Thanks

Answer 1

I solved the problem by replacing the FrameLabel with an Inset:

Column[
 {
  Show[
   Plot[ Sin[x]^2, {x, 0, Pi},
    FrameLabel -> {"", ""},
    Epilog -> {
      Inset["y", ImageScaled[{0.01, 0.55}], {0, 0}, Automatic, {0, 1}]
      },
    BaseStyle -> {FontSize -> 16, FontWeight -> Bold, 
      FontFamily -> "Calibri"},
    ImagePadding -> {{pad, pad/4}, {pad, pad/4}},
    Frame -> {True, True, True, True},
    PlotRangeClipping -> False
    ]
   , ImageSize -> 640]
  ,
  Show[
   Plot[ -Sin[x]^2/1000, {x, 0, Pi},
    FrameLabel -> {"x", ""},
    PlotRangeClipping -> False,
    Epilog -> {
      Inset["y", ImageScaled[{0.01, 0.55}], {0, 0}, Automatic, {0, 1}]
      },
    BaseStyle -> {FontSize -> 16, FontWeight -> Bold, 
      FontFamily -> "Calibri"},
    ImagePadding -> {{pad, pad/4}, {pad, pad/4}},
    Frame -> {True, True, True, True}
    ]
   , ImageSize -> 640]
  }
 ]

Which produces the following:

I saw the other solutions posted – thanks you guys, but I like my solution better, although it’s very similar to @Mr.Wizard solution. Sorry for posting the solution just now, but when I found it I couldn’t post as the site asked that I wait 8 hours before answering my own question.