acesnik
commented
6 years ago Another way to think about this is answering typical questions one would have about each task with plots and descriptive statistics: Did calibration work? Did GPTMD add any modifications? Did search find any of those modifications? How many peptides were found in search? What portion of spectra resulted in a PSM? How many peptides were identified in consolation events? How many peptides were quantified? What peptides were elevated or lower in abundance in my condition of interest (volcano plot with tooltip displays)?
rmillikin
lonelu
trishorts
I thought this idea was large enough where it should be it's own issue even though it's part of #1124 .
@acesnik wants some HTML reports and I think a lot of users really want some way to easily/graphically interpret the data coming out of MetaMorpheus/FlashLFQ.
One way to do it is to have static plots that describe things we think the user would want, i.e. ppm error over time or PSMs per file or boxplots of protein abundance.
Another way to do it is to have some kind of dynamic system that would let the user plot things that they want - i.e. define a statistic to make a box plot out of, or plot any x vs y (i.e. ppm error vs RT).
So here is an issue to centralize some ideas of what would be nice for users to have (hopefully with some input from users). I suspect this issue will never really be "closed" but is an open-ended place to suggest improvements.
We are already working on a MS2 spectrum annotator within MetaMorpheus so that particular type of plot probably doesn't belong here. We'd also have to load spectra files which I think isn't really easily doable in HTML.
Some ideas for static plots: