# 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)
