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I want to plot a few sets of data points on the same x-axis that have different units. How can I set different axes for each incompatible quantity?

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GNUplot has the ability to have 2 x- and 2 y-axes per plot. The additional axes are called x2 and y2. according to GNUplot.info FAQ

Here is a demo of it being used.

Also have a read of help plot from within the GNUplot program.

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