uplot_ratios: Molecular Formula Ratio Plot (Sample vs Control)

In ume: Ultrahigh-Resolution Mass Spectrometry Data Evaluation for Complex Organic Matter

Molecular Formula Ratio Plot (Sample vs Control)

Description

Computes the intensity ratio between a sample and a control group and visualizes it in a Van Krevelen diagram. Optionally highlights unique molecular formulas and plots the ratio distribution.

Usage

uplot_ratios(
  df,
  upper = 90,
  lower = -90,
  grp = "file_id",
  int_col = "norm_int",
  control,
  sample,
  uniques = FALSE,
  conservative = FALSE,
  palname = "ratios",
  distrib = TRUE,
  main = NA,
  plotly = FALSE,
  ...
)

Arguments

df	A data.table containing at least columns: mf, oc, hc, grouping variable grp, and intensity column int_col.
upper, lower	Ratio filtering limits (default 90 / -90)
grp	Column defining sample/control grouping
int_col	Intensity column to use
control	Character: control group name
sample	Character: sample group name
uniques	Logical: highlight uniquely present formulas
conservative	Logical: stricter uniqueness definition
palname	Color palette for projection
distrib	Logical: include ratio distribution plot
main	Optional main title
plotly	Logical: convert output plots to plotly
...	Additional arguments passed to methods.

Details

Ratio Plot in Van Krevelen Space

Value

A list with:

• ratio_table

• plot_ratio_vk

• plot_ratio_distr

See Also

Other plots: uplot_cluster(), uplot_cvm(), uplot_dbe_minus_o_freq(), uplot_dbe_vs_c(), uplot_freq_ma(), uplot_freq_vs_ppm(), uplot_hc_vs_m(), uplot_heteroatoms(), uplot_isotope_precision(), uplot_kmd(), uplot_lcms(), uplot_ma_vs_mz(), uplot_ms(), uplot_n_mf_per_sample(), uplot_pca(), uplot_reproducibility(), uplot_ri_vs_sample(), uplot_vk()

Examples

out <- uplot_ratios(
  df = mf_data_demo,
  grp = "file",
  control = "Nsea_a",
  sample  = "Fjord 01a"
)

ume documentation built on Dec. 13, 2025, 1:06 a.m.