As described here :
plot {<ranges>} {<function> | {"<datafile>" {datafile-modifiers}}} {axes <axes>} {<title-spec>} {with <style>} {, {definitions,} <function> ...}
you can see that axes are used in the plot command. After setting the ranges of your y-axes with
set yrange [y1min:y1max] set y2range [y2min:y2max]
you can specify which axis you want to use in your chart with
plot "data.txt" axes x1y1
if you want to build it with the first y axis or
plot "data.txt" axes x1y2
if you want to build it with the second y axis.
Also see this example of using multiple axes in gnuplot.
Woltan
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