How to plot several datasets with titles from one file in Gnuplot

The "-" is used to specify that the data follows the plot command. So if you use it, you'll need to do something like:

echo "set datafile separator \",\"; plot '-' using 1:2 with lines, '' using 1:3 with lines;" | cat - datafile.dat | gnuplot -p

(Quoting above probably needs to be escaped).

What're you looking for is this:

plot '< cat -'

Now, you can do:

cat test | sed ... | gnuplot -p "plot '< cat -' using ..."

Note that you might need to feed in the input data via stdin multiple times if you're using options with plot, like so:

cat testfile testfile | gnuplot -p "plot '< cat -' using 1, '' using 2"

In the above case, testfile must end with a line that has the sole character 'e' in it.

Manual reference

As documented here:

plot {<ranges>}  
      {<function> | {"<datafile>" {datafile-modifiers}}}  
      {axes <axes>} {<title-spec>} {with <style>}  
      {, {definitions,} <function> ...} 

you can see that the 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 plot with

plot "data.txt" axes x1y1

if you want to plot it against the first y-axis or

plot "data.txt" axes x1y2

if you want to plot it against the second y-axis.

Also see this example of how to use multiple axis in gnuplot.