The tool is designed as a quick way for "standard" comparison. I agree it could be nice to extend it in the future with various options, but for now it only supports the sum (for simplicity, basically). If you want to plot spin up/down curves together you will have to write a small Python script, it's really simple.
Assuming the transmission spectra are in separate files:
t1 = nlread("file1.hdf5", TransmissionSpectrum)[0]
t2 = nlread("file2.hdf5", TransmissionSpectrum)[0]
import pylab
pylab.plot(t1.evaluate(spin=Spin.Up), t1.energies(), label="File1, Spin Up")
pylab.plot(t2.evaluate(spin=Spin.Up), t2.energies(), label="File2, Spin Up")
pylab.legend()
pylab.xlabel("Transmission")
pylab.ylabel("Energy / eV")
With small modifications you can compare spin up vs down from the same file, etc.
