uplot_ma_vs_mz

Generates a UME-style scatter plot showing mass accuracy (<code>ppm</code>)
versus mass-to-charge ratio (<code>m/z</code>).
Summary statistics (median, 2.5% and 97.5% quantiles) are displayed
as horizontal reference lines and an annotation panel.
The plot is returned as a ggplot2 object by default, with optional
plotly conversion for interactivity.

Provides tools for assigning molecular formulas from exact masses
obtained by ultrahigh-resolution mass spectrometry. The methodology follows
the workflow described in Leefmann et al. (2019) <doi:10.1002/rcm.8315>.
The package supports the inspection, filtering and visualization of
molecular formula data and includes utilities for calculating common
molecular parameters (e.g., double bond equivalents, DBE). A graphical
user interface is available via the 'shiny'-based 'ume' application.

Boris Koch

Ultrahigh-Resolution Mass Spectrometry Data Evaluation for
Complex Organic Matter

uplot_ma_vs_mz function

<dl><dt>mfd</dt>
<dd>data.table with molecular formula data as derived from
<code>ume::assign_formulas</code>. Column names of elements/isotopes must match names in
the <code>isotope</code> column of <code>ume::masses</code>; values are integers representing
counts per formula.</dd>
<dt>ma_col</dt>
<dd>Character. Column containing mass accuracy (ppm).</dd>
<dt>logo</dt>
<dd>Logical. If TRUE, adds a UME caption.</dd>
<dt>plotly</dt>
<dd>Logical. If TRUE, return interactive plotly object.</dd>
<dt>...</dt>
<dd>Additional arguments passed to methods.</dd></dl>

Arguments

Plot Mass Accuracy vs m/z — uplot_ma_vs_mz

<dl>

<dt>mfd</dt>
<dd>data.table with molecular formula data as derived from
<code>ume::assign_formulas</code>. Column names of elements/isotopes must match names in
the <code>isotope</code> column of <code>ume::masses</code>; values are integers representing
counts per formula.</dd>


<dt>ma_col</dt>
<dd>Character. Column containing mass accuracy (ppm).</dd>


<dt>logo</dt>
<dd>Logical. If TRUE, adds a UME caption.</dd>


<dt>plotly</dt>
<dd>Logical. If TRUE, return interactive plotly object.</dd>


<dt>...</dt>
<dd>Additional arguments passed to methods.</dd>

</dl>

uplot_ma_vs_mz: Plot Mass Accuracy vs m/z

Description

Usage

Value

Arguments

See Also

Examples