Plot standardized feature intensities grouped by QC type

This function creates a grouped beeswarm plot of standardized feature intensities, where the y-axis represents intensity standardized such that the mean across all features is 100%. Points are grouped by qc_type and spread using quasirandom jitter.

Usage

plot_matrixeffects(
  data,
  variable = "intensity",
  qc_types = c("SPL", "TQC", "PBLK", "BQC"),
  batchwise_normalization = TRUE,
  include_qualifier = FALSE,
  only_istd = TRUE,
  include_feature_filter = NA,
  exclude_feature_filter = NA,
  min_median_value = NA,
  y_lim = c(-NA, NA),
  point_size = NULL,
  dodge_width = 0.6,
  point_alpha = 0.3,
  box_alpha = 0.3,
  box_linewidth = 0.5,
  font_base_size = NULL,
  legend_position = NULL,
  legend_size = NULL,
  show_legend_title = NULL,
  title = NULL,
  angle_x = 45
)

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.

batchwise_normalization

A logical value indicating whether to normalize the signals by batch instead of globally.

include_qualifier

A logical value indicating whether to include qualifier features. Default is TRUE.

only_istd

A logical value indicating whether to show only internal standard (ISTD) features. Default is TRUE. Set to FALSE in combination with feature_filter parameters to show other features.

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().

y_lim

A numeric vector of length 2 specifying the y-axis limits.

point_size

A numeric value indicating the size of points in millimeters. Default is 0.5.

dodge_width

Numeric. Width used to dodge overlapping points by qc_type. Default is 0.6.

point_alpha

Numeric. Transparency of the plotted points. Default is 0.3.

box_alpha

Numeric. Transparency of the boxplot. Default is 0.3.

box_linewidth

Numeric. Width of the boxplot lines. Default is 0.5.

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.

angle_x

Numeric. Angle of the x-axis text labels. Default is 45.

Value

A ggplot object showing the grouped standardized beeswarm plot.

See also

Other QC plots: plot_feature_correlations(), plot_interference_correction(), plot_normalization_qc(), plot_pca(), plot_pca_loading(), plot_qc_interference_impact(), plot_qc_summary_byclass(), plot_qc_summary_overall(), plot_qcmetrics_comparison(), plot_rla_boxplot(), plot_rt_vs_chain(), plot_runscatter(), plot_runsequence()