main_docu: Common parameters for ume package functions

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

Common parameters for ume package functions

Description

Central place to document arguments (e.g., msg, pl, formula_library) that are inherited by multiple functions via ⁠@inheritParams main_docu⁠. This is not a user-facing function and is only provided for documentation reuse.

Arguments

formula_library	Molecular formula library: a predefined data.table used for assigning molecular formulas to a peak list and for mass calibration. The library requires a fixed format, including mass values for matching. Predefined libraries are available in the R package ume.formulas and further described in Leefmann et al. (2019). A standard library for marine dissolved organic matter is ume.formulas::lib_02. New libraries can be built using ume::create_ume_formula_library().
grp	Character vector. Names of columns (e.g., sample or file identifiers) used to aggregate results.
i_magnitude	String. Name of the column that contains peak intensity information (default: "i_magnitude").
known_mf	data.table with known molecular formulas (ume::known_mf).
masses	A data.table. Defaults to ume::masses (based on NIST data) containing isotope information for elements, including nominal and exact mass, relative abundance, and Hill system order.
mf	Character vector of molecular formula(s) (e.g., c("C10H23NO4", "C10H24N4O2S")).
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.
msg	logical. Deprecated synonym for verbose.
verbose	logical; if TRUE, show progress messages.
mz	String. Name of the column that contains mass-to-charge information (default: "mz").
pl	data.table containing peak data. Mandatory columns include neutral molecular mass (mass), peak magnitude (i_magnitude), and a peak identifier (peak_id).
logo	Logical. If TRUE, adds a UME caption.
palname	Color palette name for f_colorz() (viridis, magma, plasma, etc.).
nice_labels	Logical. If true (default) axis/legend labels are generated from ume::nice_labels_dt.
col_bar	Logical. If TRUE, adds a color legend (default is TRUE).
plotly	Logical. If TRUE, return interactive plotly object.
int_col	Character. The name of the column that contains the intensity values to be used (e.g. for clustering or color coding). Default usually is "norm_int" for normalized intensity values.
tf	Logical. If TRUE, applies a transformation to the color scale (default is FALSE).
size_dots	Numeric. Size of the dots in the plot (default = 0.5).
gg_size	Base text size for theme_uplots(). Default = 12.
cex.axis	Numeric. Size of axis text (default is 1).
cex.lab	Numeric. Size of axis labels (default is 1.4).
z_var	Character. Column name for variable used for color-coding. Content of column should be numeric.
...	Additional arguments passed to methods.

Details

Use ⁠@inheritParams main_docu⁠ in other functions to pull in these definitions. This topic is marked internal so it does not clutter the index.

License

This package is released under the MIT License. See the LICENSE file for details.

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