When having a look at peak areas with “log scale” activated, idopt value for the highest amount is not visible (both in standard and replicate view).

Yuval, you could take this one. Alex partly fixed the issue of idotp truncation in this graph over the summer, but it looks like his fix isn't working in log scale.

Apparently y-axis scrolling to view the idopt values is also problematic when log scale is on.

This is more your area now, and you have already fixed the scroll wheel problem.

Nick, I think you had thoughts about this one and other issues with Log scale in the Peak Areas plot.

Skyline currently prevents you from having a log scale Y-axis when displaying Ratio to Heavy or Ratio to Global Standards. The reason that we disabled that is that there were a few quirky things going on. Once we fix those quirky things we should allow this again.

The things that go wrong are:
1. The plot is completely blank if the maximum value displayed on the graph is less than 1. This is because Skyline sets the y axis scale min to 1, but leaves the y axis scale max as "auto". If ZedGraph decides that the maximum on the scale is less than the min, the graph ends up being completely blank.
2. Stacked bar graphs do not look right when the the Y-axis is a logarithm. If it's set to "Transitions > All" and it's a log plot, it needs to look the same as "Transitions > Total".
3. Make sure that the selection box is drawn in the right spot. It's tricky to figure out how tall it should be because of the logarithms involved.

Skyline issues have moved to GitHub Issues at https://github.com/ProteoWizard/pwiz/issues
Issues will be ported as necessary for active work.