Creates a 3D LC–MS plot (RT x m/z x intensity) when retention time is available.
If no retention-time column exists (e.g., with DI-FTMS demo data), the function
gracefully falls back to uplot_ms() and issues an informative message.
uplot_lcms(
pl,
mass = "mz",
peak_magnitude = "i_magnitude",
retention_time = "ret_time_min",
label = "file_id",
logo = FALSE,
...
)A plotly 3D visualization (LC-MS) or a 2D MS spectrum fallback.
data.table containing peak data. Mandatory columns include neutral
molecular mass (mass), peak magnitude (i_magnitude), and a peak
identifier (peak_id).
Column containing m/z values (default "mz").
Column containing intensity (default "i_magnitude").
Column with retention time (default "ret_time_min").
Sample/group labeling column (default "file_id").
Logical. If TRUE, adds a UME caption.
Additional arguments passed to methods.
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_ma_vs_mz(),
uplot_ms(),
uplot_n_mf_per_sample(),
uplot_pca(),
uplot_ratios(),
uplot_reproducibility(),
uplot_ri_vs_sample(),
uplot_vk()