uplot_vk: uplot_vk

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

uplot_vk

Description

Creates a Van Krevelen diagram (H/C vs O/C).

Usage

uplot_vk(
  mfd,
  z_var = "norm_int",
  nice_labels = TRUE,
  projection = TRUE,
  palname = "viridis",
  median_vK = TRUE,
  col_median = "white",
  ai = TRUE,
  logo = TRUE,
  size_dots = 3,
  col_bar = TRUE,
  tf = FALSE,
  cex.axis = 12,
  cex.lab = 15,
  plotly = FALSE,
  ...
)

Arguments

mfd	data.table with molecular formula data as derived from ume::assign_formulas. Column names of elements/isotopes must match names in the isotope column of ume::masses; values are integers representing counts per formula.
z_var	Character. Column name for variable used for color-coding. Content of column should be numeric.
nice_labels	Logical. If true (default) axis/legend labels are generated from ume::nice_labels_dt.
projection	If TRUE, median z-values per (oc,hc) are used.
palname	Color palette name for f_colorz() (viridis, magma, plasma, etc.).
median_vK	Add median VK point.
col_median	Color of the marker for the median O/C and H/C value (Default = "white")
ai	Add aromaticity index threshold lines.
logo	Logical. If TRUE, adds a UME caption.
size_dots	Numeric. Size of the dots in the plot (default = 0.5).
col_bar	Logical. If TRUE, adds a color legend (default is TRUE).
tf	Logical. If TRUE, applies a transformation to the color scale (default is FALSE).
cex.axis	Numeric. Size of axis text (default is 1).
cex.lab	Numeric. Size of axis labels (default is 1.4).
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

Plot Van Krevelen Diagram

Value

ggplot or plotly object

References

Van Krevelen D. (1950). Graphical-statistical method for the study of structure and reaction processes of coal. Fuel, 29, 269-284.

Kim S., Kramer R.W., Hatcher P.G. (2003). Graphical method for analysis of ultrahigh-resolution broadband mass spectra of natural organic matter, the Van Krevelen Diagram. Analytical Chemistry, 75, 5336-5344. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/ac034415p")}

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_ratios(), uplot_reproducibility(), uplot_ri_vs_sample()

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