Scatter: CN-bundle m/z vs RT error with dynamic-filter cutoffs — plot_compare_pave_lib_assignment_error

Points are coloured by manual review group: overlap, wrong in PAVE, wrong in TRACE, and filter out to noise (from type/reason in the assignment table). Dashed lines mark ppm.dyn (horizontal) and rt.tol.dyn (vertical) from object@advancedAna$TRACE_temp.

Usage

plot_compare_pave_lib_assignment_error_scatter(
  assignment,
  object,
  i.pol = 0,
  mz_error = c("max", "mean"),
  scatter_groups = .compare_pave_lib_assignment_scatter_levels(),
  return.data = FALSE
)

Arguments

assignment: Path to assignment xlsx or data frame (see [compare_pave_lib_assignment_error_data()]).
object: MSdev object with TRACE CNfinder results.
i.pol: Polarity index. `0` for negative and `1` for positive.
mz_error: Use `"max"` or `"mean"` across CN-bundle edges.
scatter_groups: Character vector of scatter groups to include (see [compare_pave_lib_assignment_error_data()]).
return.data: If `TRUE`, return list with `plot`, `data`, `ppm.dyn`, and `rt.tol.dyn`.

Value

A `ggplot` object, or a list when `return.data = TRUE`.