introduce a `TICxIT` column in default aggregator and rename `agc_xxx` parameters in `orbi_flag_outliers`

[sebkopf]

2 parts to this:

1

the tic * it.ms quantity is used so frequently, it seems sensible to have the default aggregators in isoorbi simply introduce the column TICxIT = tic * it.ms/1000 which is useful because it can also be directly compared to agcTarget having the same units operationally (a number that reflects injected ion count). This makes it then easy to plot agg_data |> orbi_plot_raw_data(y = TICxIT / agcTarget) + scale_y_continuous(labels = scales::label_percent()) (or maybe allow agg_data |> orbi_plot_raw_data(y = TICxIT / agcTarget, y_scale = "percent")) ).

key question: should it be ticxit, ticXit or TICxIT @123caj @elliottmueller?

2

the agc_xxx parameters in orbi_flag_outliers are really misnomers since agc (automatic gain control) is not what is being used here for cutoffs, it's really the TICxIT so these should be renamed to e.g. TICxIT_absolute_cutoff (which is agc_absolute_cutoff/1000), TICxIT_percentage_cutoff (which is the same as agc_window) and TICxIT_fold_cutoff (which is the same as agc_fold_cutoff).

@FR86: does this seem like a sensible direction (the old parameters would still work, just have a deprecation warning)

[FR86]

Sure, the rename sounds reasonable.
TICxIT reads cleanest to me. When you argue that after shifting from milliseconds to seconds we're having the same units compared to agcTarget, doesn't that make the next logical step to express it as a fraction of agcTarget and talk about an ion fill ratio or something?

[sebkopf]

yes, we were thinking about another column like that that is also automatically calculated in the default aggregator, something like agcCheck = TICxIT / agcTarget (agcCheck was the name suggested by @elliottmueller ). Then it could likewise be even more easily plotted with orbi_plot_raw_data(y = agcCheck). Thoughts @FR86 ?