uplot_pca: uplot_pca

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

uplot_pca

Description

This function performs Principal Component Analysis (PCA) on a dataset, and visualizes the results in various ways, including a scatter plot of the first two principal components (PC1 vs PC2) and a Van Krevelen plot projected using PC1 values. The PCA is performed on the molecular formula data, aggregated by a grouping variable, and handles cases where columns exhibit zero variance (which cannot be included in PCA).

Usage

uplot_pca(
  mfd,
  grp,
  int_col = "norm_int",
  palname = "viridis",
  col_bar = TRUE,
  ...
)

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.
grp	Character vector. Names of columns (e.g., sample or file identifiers) used to aggregate results.
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.
palname	Color palette name for f_colorz() (viridis, magma, plasma, etc.).
col_bar	Logical. If TRUE, adds a color legend (default is TRUE).
...	Additional arguments passed to methods.

Details

Principal Component Analysis (PCA) Plotting

Value

A list containing:

pca	The PCA model object (class prcomp).
t_score	A data table of PCA scores (principal component values for each sample).
fig_vk	A Van Krevelen plot projected with PC1 values.
fig_pca	A scatter plot of the first two principal components (PC1 vs PC2).
mfd	The input data table, augmented with principal component values.

Note

The function uses prcomp for PCA and uplot_vk for the Van Krevelen plot.

See Also

uplot_vk for the Van Krevelen plot function.

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_ratios(), uplot_reproducibility(), uplot_ri_vs_sample(), uplot_vk()

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