uplot_kmd: Kendrick Mass Defect (KMD) vs. Nominal Mass Plot

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

Kendrick Mass Defect (KMD) vs. Nominal Mass Plot

Description

This function generates a scatter plot of Kendrick Mass Defect (KMD) versus nominal mass (nm), with color-coding based on a specified variable (z_var). Optionally, the plot can be returned as an interactive Plotly object.

Usage

uplot_kmd(
  df,
  z_var = "norm_int",
  palname = "redblue",
  size_dots = 0.5,
  col_bar = TRUE,
  tf = FALSE,
  logo = TRUE,
  cex.axis = 12,
  cex.lab = 15,
  plotly = FALSE,
  ...
)

Arguments

df	A data.table or data.frame containing columns: nm (nominal mass) kmd (Kendrick mass defect) the color variable given in z_var.
z_var	Character. Name of the column used for color mapping.
palname	Character. Palette name passed to f_colorz().
size_dots	Numeric. Point size.
col_bar	Logical. (Reserved for future use; currently ignored.)
tf	Logical. (Reserved for future use; currently passed to f_colorz() via ... if desired.)
logo	Logical. If TRUE, adds a UME caption.
cex.axis	Numeric. Axis text size.
cex.lab	Numeric. Axis label size.
plotly	Logical. If TRUE, return interactive plotly object.
...	Arguments passed on to f_colorz z Numeric vector. Values whose colors should be computed. col_num Integer. Number of colors in the palette (default: 100). verbose logical; if TRUE, show progress messages.

Details

Kendrick Mass Defect (KMD) vs. Nominal Mass Plot

Value

A ggplot object (or a plotly object if plotly = TRUE) showing KMD vs nominal mass.

References

Kendrick E. (1963). A mass scale based on CH_2 = 14.0000 for high resolution mass spectrometry of organic compounds. Analytical Chemistry, 35, 2146–2154.

Hughey C.A., Hendrickson C.L., Rodgers R.P., Marshall A.G., Qian K.N. (2001). Kendrick mass defect spectrum: A compact visual analysis for ultrahigh-resolution broadband mass spectra. Analytical Chemistry, 73, 4676–4681. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/ac010560w")}

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_lcms(), uplot_ma_vs_mz(), uplot_ms(), uplot_n_mf_per_sample(), uplot_pca(), uplot_ratios(), uplot_reproducibility(), uplot_ri_vs_sample(), uplot_vk()

Examples

uplot_kmd(mf_data_demo, z_var = "norm_int", plotly = TRUE)

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