Plot PCA loadings

Generates a plot of PCA loadings, illustrating the contribution of features to each principal component. This function can be used to investigate which feature (groups) are contributing to the variance seen in the plot and which need further investigation.

Usage

plot_pca_loading(
  data = NULL,
  variable,
  qc_types = NA,
  pca_dims = c(1, 2, 3, 4),
  log_transform = TRUE,
  top_n = 30,
  vertical_bars = FALSE,
  abs_loading = TRUE,
  filter_data = FALSE,
  include_qualifier = FALSE,
  include_istd = FALSE,
  include_feature_filter = NA,
  exclude_feature_filter = NA,
  min_median_value = NA,
  font_base_size = NULL,
  legend_position = NULL,
  legend_size = NULL,
  show_legend_title = NULL,
  title = NULL,
  strip_text_size = NULL,
  strip_bg_color = NULL,
  legend_bg_alpha = NULL
)

Arguments

data: A MRMhubExperiment object.
variable: A character string indicating the variable to use for PCA analysis. Must be one of: "area", "height", "intensity", "norm_intensity", "response", "conc", "conc_raw", "rt", "fwhm".
qc_types: A character vector specifying the QC types to plot. It must contain at least one element. The default NA plots any of the non-blank QC types ("SPL", "TQC", "BQC", "HQC", "MQC", "LQC", "NIST", "LTR") present in the dataset.
pca_dims: A numeric vector indicating for which PCA dimensions the loadings should be shown. Default is c(1, 2, 3, 4).
log_transform: A logical value indicating whether to log-transform the data before the PCA. Default is TRUE.
top_n: Number of top features with highest absolute loading that will be shown for each PC dimension. Default is 30.
vertical_bars: Show vertical bars instead of horizontal bars in the plot. Default is FALSE.
abs_loading: Show absolute loading values instead of signed loadings. Default is TRUE.
filter_data: A logical value indicating whether to use all data (default) or only QC-filtered data (filtered via filter_features_qc()).
include_qualifier: A logical value indicating whether to include qualifier features. Default is TRUE.
include_istd: A logical value indicating whether to include internal standard (ISTD) features. Default is TRUE.
include_feature_filter: Feature(s) to include by feature_id, as a character vector. Each element is matched exactly when it names an existing feature, otherwise treated as a regex; elements combine with OR. A full ID (e.g. "S1P d18:0 [M>60]") needs no escaping, while patterns like "PC|PE" still work. NA or "" ignores the filter.
exclude_feature_filter: Feature(s) to exclude by feature_id, matched the same way as include_feature_filter. NA or "" ignores the filter.
min_median_value: Minimum median feature value across the selected QC-type samples required for a feature to be included. NA (default) applies no filtering. This is a fast way to exclude noisy features; for principled QC-based filtering use filter_features_qc().
font_base_size: Numeric. Base font size (in points) for plot text; all plot text scales proportionally with this value. NULL (default) uses the global default set by mrmhub_set_plot_defaults() if one is in effect, otherwise an automatic size (derived from the facet-column count on paged plots, or the per-plot default shown in the Usage section above).
legend_position: Optional legend placement. One of "right", "left", "top", "bottom", "none"; a corner keyword "inside-tr", "inside-tl", "inside-br", "inside-bl"; or a numeric c(x, y) in [0, 1] coordinates. NULL (default) keeps the current placement, unless a global default is set with mrmhub_set_plot_defaults().
legend_size: Optional single multiplier of font_base_size (when <= 3) or absolute point size (when > 3) that scales the whole legend: text, title, key and the plotted symbols. NULL (default) leaves the legend unchanged.
show_legend_title: Logical. NULL (default) keeps the legend title, unless a global default is set with mrmhub_set_plot_defaults(); FALSE hides it, TRUE forces it shown.
title: Optional plot title. NULL (default) or NA shows no title; a character string is shown as the title.
strip_text_size: Optional facet strip text size, as a multiplier of font_base_size (when <= 3) or an absolute point size (when > 3). NULL (default) inherits from font_base_size.
strip_bg_color: Optional facet strip background fill colour. The strip text colour is set automatically for contrast (white on a dark fill, black on a light one). NULL (default) keeps the house dark-navy strips.
legend_bg_alpha: Optional opacity ([0, 1]) of a white legend background box, useful for a readable inside legend drawn over points. NULL (default) leaves the legend background unchanged.

Value

A ggplot object with PCA loadings plot

Usage

Arguments

Value

See also