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Since Dimension 1 is longer than the Dimension 2, I want to make the plot vertically long rather than horizontally long so that it's easier to include it in my thesis. But is it acceptable to make Dimension 1 the y axis and not the x axis?

Ian
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    No, only the x axis is acceptable. Additionally, if I see you printing the graphic out on the x-axis and handing it out to people sideways (such that it is effectively the y-axis), we will have no choice but to retract your MDS privileges ;)

    In all seriousness, you can put whatever you want on any axis you want so long as it effectively communicates your point. (Also consider that running MDS with general metrics will return arbitrarly rotated data for most solvers, and no one worries about which axis is where).

     – John Madden Aug 20 '22 at 16:54

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