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Plot TRACE CN labeling fraction per metabolite and sample

Source: R/TRACE_workflow.R
plot_TRACE_labeling_fraction.Rd

For each TRACE metabolite seed, counts all CN-labeled features in the seed network (C0N0, C0Ny, CxN0, CxNy, and other matched CxNy patterns) and calculates the labeling fraction in each sample:

  • `S12C14N`: C0N0 / total

  • `S12C15N`: C0Ny / total

  • `S13C14N`: CxN0 / total

  • `S13C15N`: CxNy / total

Usage

plot_TRACE_labeling_fraction(
  object,
  i.pol = 0,
  TRACE_cor_cutoff = 0.7,
  return.data = FALSE
)

Arguments

object

MSdev object with TRACE results in `object@advancedAna$TRACE` and CN hits in `object@advancedAna$TRACE_temp`.

i.pol

Polarity index. `0` for negative and `1` for positive.

TRACE_cor_cutoff

Minimum `TRACE_cor` used to select CN seeds when TRACE metabolite annotations are unavailable.

return.data

Logical. If `TRUE`, return a list with `plot` and `data`.

Value

A patchwork object combining the box/point plot and density plot, or a list with `plot`, `p1`, `p2`, and `data` when `return.data = TRUE`.