If you run TestDiaTtofTutorial and show View > Peak Areas > Relative Abundance the plot that comes up initially includes everything in the document both Targets and Decoys.

We should add a "Points" submenu to the right-click menu, like we have for the Retention Times - Regression plot:

Points>
  Targets
  Targets at 1% FDR
  <Standards>
  Decoys

We should drop the "Standards" for this plot, since it is referring to iRT standards in the Retention Times - Regression plot.

But, in this use case of DIA with an mProphet model, the other 3 options make a lot more sense than what we are currently showing in this plot.

You can kind of get some of this with the "Exclude" submenu which contains "Standards" and "Lists", as long as you don't have your decoys in a list, then excluding Lists excludes the decoys, but this is problematic because it is not the default and documents may be made up of just two lists: all targets and all decoys.

It will be much better to implement this Points option and have it default to Targets as it does for the Retention Times - Regression plot. Then, the user can explore the other point sets by choosing them.

I'm not sure this is true anymore. The relative abundance plot does not display any decoys. There are 146 non-decoy peptides in the document and the highest rank in the plot is 146. Not sure if we still need to fix this one. Unless there are use cases where we want explicitly to include the decoys.

This seems to have been incidentally fixed by PR #3020 on June 19th.

At the time this bug was opened, when displaying "peptides", the relative abundance plot used to display one point per Precursor and would use the "Total Area" value.

PR #3020 changed it so it has one point per Peptide and uses the "Normalized Area" value.
The "Normalized Area" value for a decoy peptide is always null so decoy peptides will not show up on that graph.

Also, when displaying "proteins", the decoy peptide list would never have been displayed because it was using the Protein Abundance value which is also null for the decoy peptide list.