Plot XIC comparison for dynamic-filtered vs overlap CN seeds — plot_compare_pave_dyn_filtered

For each feature, resolves the TRACE CN bundle and filters each CN form (C0N0, CxN0, C0Ny, CxNy) by its own feature mzmed +/- mz_ppm and shared rtmed +/- rt_window.

Usage

plot_compare_pave_dyn_filtered_xic(
  feature_id,
  object,
  i.pol = 0,
  comparison_feature_id = NULL,
  rt_window = 20,
  mz_ppm = 10,
  sampleNames = NULL,
  return.data = FALSE
)

Arguments

feature_id: CN seed feature ID removed by TRACE dynamic filter.
object: MSdev object with processed xcms data and TRACE results.
i.pol: Polarity index. `0` for negative and `1` for positive.
comparison_feature_id: Optional retained CN seed for the right panel.
rt_window: RT half-window in seconds; sets rtr = rtmed +/- rt_window for filterRt() and the XIC x-axis (xlim).
mz_ppm: m/z half-window in ppm; sets mzr = mzmed +/- mz_ppm for filterMz() (default 5).
sampleNames: Ignored; one representative sample per CN group is used.
return.data: If TRUE, return a list with plot and data.

Value

A single-column patchwork object (p1 chrom + four m/z strips) for feature_id, or a list when return.data = TRUE. Comparison metadata for the overlap seed is still returned in data when return.data = TRUE.