main_docu: 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.

License

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

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.