PrepOrbiData.R - Additional data processing outputs

[j-e-hunter]

I think that having preporbidata spit out additional processing information, for example fitted peaks, more detailed alignment diagnostics would be very helpful in validating the dataset fed to lobstahs.

[jamesrco]

So, in the current script, you can edit lines 430-492 (currently commented out) to generate and then selectively plot some peaks from a given sample. I have used this before, choosing a few peaks at random for inspection. You can also just use the sleep argument when calling xcmsSet: If you set it to something other than "0," the function will generate periodic plots of whatever spectrum it is working on at the time and push them to your display. However, I found this didn't work properly with the graphics engine in the Mac version of RStudio. It appeared to work ok when running R directly from the console or command line.