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With matlab you just need the mindset that nothing works like you think it does. Then you'll do fine.

endor651168d@sweetnothings they are discrete. Both x and y are discrete 1D arrays, and Z is a 2D matrix.
Hence my confusion when it decides to use the x axis to access columns and y axis to access rows, instead of the other way around (as I'd expect from the Z(x, y) notation). 
endor651168d@sweetnothings look at element a(3,4) of the matrix: the reported position is (x=4, y=3)

endor651168d@sweetnothings you mean like this?
I can see why you would represent things that way in your example, but what you've essentially described is a lefthanded coordinate system.
Sure, it's mathematically coherent, but it seems like a weird 'default' choice to represent an arbitrary set of data, given that most [citation needed] people work with righthanded coordinate systems.
Or at least, in my field of study (aerospace engineering), the most common assumption I see is that we're working with a RH coordinate system.
Given that assumption, using a LH system for a surface plot seems a very odd design choice to me  even for a more 'mathematically inclined' tool like Matlab (referring to stuff like array indices starting from 1 rather than 0).
But maybe I'm assuming wrong? Are LH systems far more common when representing data like this? Or am I misreading your axes? 
endor651168d@sweetnothings lol, that excel plot is actually righthanded if you look at the data. Even if you transpose the matrix, it's still readable.
In my example, matlab swapped the axes but pretended like it didn't. So a(x=3, y=4) gets labeled a(x=4, y=3) in the plot.
So it didn't just flip the axes around, it actually swapped data between x and y. That's inconsistent.
You can see that if you try to look at element (1,32), which is in position (32, 1) in the plot  it's not respecting the axes that I've given it.
Thank you Matlab, for my daily dose of frustration.
Thank you Matlab, for deciding to surfaceplot a 2D variable with the x axis = columns and y axis = rows, because of course that's the most intuitive way to go about it.
Because of course that's consistent with the standard way to refer to a variable's elements.
After all, everybody knows that Z(i, j) refers to the ith column and jth row of a matrix, right?
Thank you, Matlab, for depriving me of the little fuck I gave about getting something done today.
Now go die in a fire.
rant
matlab must die
i hate you more than facebook