Plot highly correlated feature pairs

Creates scatter plots for pairs of features that have correlations outside specified thresholds. Each pair is displayed in a separate facet with its correlation coefficient.

This plot can be used to visually inspect highly correlated features, that may represent duplicate identifications or represent isomers.

Usage

plot_feature_correlations(
  data,
  variable,
  qc_types = NA,
  cor_min,
  cor_min_neg = -0.99,
  log_scale = FALSE,
  sort_by_corr = TRUE,
  filter_data = FALSE,
  include_qualifier = FALSE,
  include_istd = FALSE,
  include_feature_filter = NA,
  exclude_feature_filter = NA,
  min_median_value = NA,
  output_pdf = FALSE,
  path = NA,
  return_plots = FALSE,
  rows_page = 4,
  cols_page = 5,
  specific_page = NA,
  page_orientation = "LANDSCAPE",
  point_size = 1,
  point_alpha = 0.8,
  point_stroke = 0.3,
  line_width = 0.5,
  line_color = "orange",
  line_alpha = 0.5,
  font_base_size = 8,
  show_progress = TRUE
)

Arguments

data: A MRMhubExperiment object.
variable: A character string indicating the signal variable to plot. 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.
cor_min: Numeric. Minimum correlation threshold. Only feature pairs with positive correlations above this value will be shown. Set to Inf to exclude positive corrections.
cor_min_neg: Numeric. Minimum nagative correlation threshold. Only feature pairs with negative correlations above this value will be shown. Set to -Inf to exclude nagative corrections.
log_scale: A logical value indicating whether to use a log10 scale for both axes. Default is FALSE.
sort_by_corr: A logical value indicating whether to sort the features in the plot by correlation or alphabetically by feature ID. 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: A regex pattern or a vector of feature names used to filter features by feature_id. If NA or an empty string ("") is provided, the filter is ignored. When a vector of length > 1 is supplied, only features with exactly these names are selected (applied individually as OR conditions).
exclude_feature_filter: A regex pattern or a vector of feature names used to exclude features by feature_id. If NA or an empty string ("") is provided, the filter is ignored. When a vector of length > 1 is supplied, only features with exactly these names are excluded (applied individually as OR conditions).
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().
output_pdf: If TRUE, saves the generated plots as a PDF file. When FALSE, plots are directly plotted.
path: The file path for saving the PDF. Must be defined if output_pdf is TRUE.
return_plots: Logical. If TRUE, returns the plots as a list of ggplot objects.
rows_page: Number of rows of plots per page.
cols_page: Number of columns of plots per page.
specific_page: An integer specifying a specific page to plot. If NA (default), all pages are plotted.
page_orientation: Orientation of the PDF paper: "LANDSCAPE" or "PORTRAIT".
point_size: A numeric value indicating the size of points in millimeters. Default is 1.
point_alpha: A numeric value indicating the transparency of points (0-1). Default is 0.8.
point_stroke: A numeric value indicating the stroke width of the points. Default is 0.3.
line_width: A numeric value indicating the size of the correlation line. Default is 0.5.
line_color: A character string indicating the color of the correlation line. Default is orange.
line_alpha: A numeric value indicating the transparency of the correlation line (0-1). Default is 0.5.
font_base_size: Numeric. Base font size (in points) for plot text. Default is 8.
show_progress: Logical. If TRUE, displays a progress bar during plot creation.

Value

A ggplot object showing scatter plots of highly correlated feature pairs. Returns NULL if no correlations meet the threshold criteria.

Usage

Arguments

Value

See also