[x] Think of a better name for add_peaklist_rect. The syntax (plot(sample) + add_peaklist_rect(plot(sample),peaklist)) is weird. Can it be refactored to plot(sample) + geom_peaklist(peaklist) or since we also add a scale plot(sample)+overlay_peaklist(peaklist)?
[x] getChromatogram() and getSpectrum() should let us choose the aggregation function. So we can choose to either sum drifts (or retentions) or get the one with higher intensity in the range.
[ ] getChromatogram() and getSpectrum() for GCIMSDataset objects. Maybe they have to return MChromatogram and MSpectrum objects, with a plot method? This could simplify smoothing and baseline plots in the vignette. These objects could also have a copy of pData(dataset) so the plot can use annotations. This would cover an implementation for getRIC(), getTIS(), plotRIC(), plotTIS() for GCIMSDataset objects.
[x] After realize() we should save the dataset object in the folder as well, so we can import the directory . An import function that takes such directory and changes the base_dir if it has been moved would be desirable.
[x] Add examples and documentation on how to add a realize action
Reading data
[x] Helpers for importing CSV files that are not overly specific to a software version
[ ] Support nos/scm files
Physical units:
[ ] Peak intensity in volts vs a.u.
[ ] Support for reduced mobility units. Replace dt_range with ims_range and ims_unit ?
[ ] Support for retention index units. rt_range -> gc_range & gc_unit ?
[x] find_rip verbosity information prints too many significant digits on drift time limits
Internal and external standards
[ ] Conversion from Retention time to Retention index using additional samples (ketones mixture)
[ ] Usage of internal standards (e.g. 4-fluorobenzaldehyde) for QC
[ ] Plots showing the stability of the daily pools, if available
Plots
[ ] plot(dataset, sample, dt_range, rt_range) (several samples in subplots, same intensity scale)
[ ] align should save RIC and TIS before transforming samples, so we can get a before and after plot of them
Vignette and docs:
[ ] Review vignette plots
[ ] Each generic in its own help page, with a @family name-of-generic tag. Each method with the same family tag. This will make help pages easier to browse.
[ ] Review docs from:
[ ] plot for GCIMSChromatogram and GCIMSSpectrum
[ ] tidy for GCIMSSample
[x] add_peaklist_rect
[ ] create_annotations_table
[ ] getIMS, getChromatogram
[ ] integratePeaks
[ ] peaks
[x] Runnable examples for > 80% of functions of the new API
These to-dos are leftovers from #13
To do things:
[x] Think of a better name for
add_peaklist_rect. The syntax (plot(sample) + add_peaklist_rect(plot(sample),peaklist)) is weird. Can it be refactored toplot(sample) + geom_peaklist(peaklist)or since we also add a scaleplot(sample)+overlay_peaklist(peaklist)?[x]
getChromatogram()andgetSpectrum()should let us choose the aggregation function. So we can choose to either sum drifts (or retentions) or get the one with higher intensity in the range.[ ]
getChromatogram()andgetSpectrum()forGCIMSDatasetobjects. Maybe they have to return MChromatogram and MSpectrum objects, with a plot method? This could simplify smoothing and baseline plots in the vignette. These objects could also have a copy ofpData(dataset)so the plot can use annotations. This would cover an implementation forgetRIC(),getTIS(),plotRIC(),plotTIS()forGCIMSDatasetobjects.[x] After realize() we should save the dataset object in the folder as well, so we can import the directory . An import function that takes such directory and changes the base_dir if it has been moved would be desirable.
[x] Add examples and documentation on how to add a realize action
Reading data
Physical units:
dt_rangewithims_rangeandims_unit?Internal and external standards
Plots
plot(dataset, sample, dt_range, rt_range)(several samples in subplots, same intensity scale)Vignette and docs:
@family name-of-generictag. Each method with the same family tag. This will make help pages easier to browse.