In IsoCor: Analyze Isotope Ratios in a 'Shiny'-App

Plot options

Plot window shows intensity vs time plot according to the processing mode selected:\ IR mode: intensity of MI on y axis, RT on x axis. Intensity of SI and IR values can superimposed by clicking the checkbox (see below).\ IDMS mode: intensity of MF on y axis, RT on x axis.

Explanation of checkboxes:

show all samples: when checked all data files are shown on the plot; when unchecked, then new dropdown menu appears where user can select one specific file to be shown on the plot\
show peak boundaries: show/hide boundaries (start and end) of the detected peaks; the boundaries are shown as vertical lines\
show sample IDs: show/hide sample names (file names); the color of the sample name text matches with the color of the corresponding curve\
overlay SI trace: show/hide intensities of SI (secondary isotope) on the plot; by default only MI intensity is shown (inactive in IDMS mode)\
overlay ratio points: show/hide isotope ratio values calculated (with PBP method) for each peak (inactive in IDMS mode)\
correct ratio points: show/hide corrected isotope ratio values after mass bias is correction applied (inactive in IDMS mode).

Explanation of buttons:

cut range: this option helps to cut out edges of the data; for example, when start and end of the measurement are too noisy, then by cutting them out we can improve baseline correction. To cancel the cut, click "undo cut"
align rt: align retention time of the samples to improve visualization of the samples; aligning doesn't affect any calculation
filter points: quantile filter for IR value to improve visibility of the points by removing the outliers at both ends of the peaks (inactive in IDMS mode)