how to flip and combine two spectra for comparison

I want to compare two spectra. What I do is multiply the Y axis of one of the spectra with -1 and then plot both the spectra on the same figure. It is good to compare but look bad while I present. Because the intensity axis of one spectra appear negative values. Is there any other way to code so that I can get spectra look like the one in the attached image?

This example I downloaded from internet. Here Y axis of both the spectra shows the real intensity.

Answer 1

[Walter Roberson]

You could normalize each spectrum perhaps.

plot(time, spectrum1 ./ max(spectrum1), time, -spectrum2 ./ max(spectrum2))

[aneps]

Thank you. But I dont want to normalize. I want absolute values. Just the spectra need to be plotted on the same figure with the second one flip. Also, in this case, the intensity of the spectrum2 appears in negative. This is what I already have, I want to get rid of those negative values and show the real positive values for the intensity but at the same time flipped with respect to the spectrum1

[Walter Roberson]

Suppose one of the values in the (mostly positive) spectrum is -1000. Then at that point, do you want to substitute 0? Or do you want to take abs() of all the values, and then take the negative of one of the two spectra, in which case you would not be able to tell the difference between a positive spike and a negative spike within any one signal?

[aneps]

The spectra I have does not have negative values, because the Y axis is counts (only positive values or 0). I am not sure if you did not understand my question correctly. I am sorry. My question was, I have two spectra (X axis mass to charge ratio, Y axis number of counts). I want to plot those two in the same figure with one spectra flipped,exactly like in the attached image. The attached image here is the plot I tried to make. I tried to flip one spectra by multiplying -1 on the Y axis of the second spectra. Here the Y axis of the flipped spectra is in negative values. I want the spectra to be like this BUT Without Negative values, means, the original positive values on the flipped spectra also.

[Walter Roberson]

Oh, this is all about the labeling of the second plot?

In that case, use plotyy(), or the more modern yyaxis(), and set the bottom one to have 'YDir', 'reverse'. For example,

ax1 = subplot(2,1,1); plot(x,y1)
ax2 = subplot(2,1,2); plot(x,y2)
linkaxes([ax1,ax2],'x')
set(ax2,'YDir','reverse')
pos1 = get(ax1,'Position');
set(ax2,'Position', [pos1(1) pos1(2)-pos1(4), pos1(3), pos1(4)])
set(ax1,'XTick',[])

[aneps]

Thank you very much.... This is exactly what I want!