Plot the results of interference correction

This function generates grouped standardized beeswarm plots to visualize the results of interference correction across different QC types.

Usage

plot_interference_correction(
  data,
  qc_types = c("SPL", "TQC", "PBLK", "BQC"),
  include_qualifier = FALSE,
  include_istd = TRUE,
  include_feature_filter = NA,
  exclude_feature_filter = NA,
  min_median_value = NA,
  min_correction_pct = NA,
  sort_by_effect = c("none", "desc", "asc"),
  top_n = 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.

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.

include_qualifier

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

include_istd

A logical value indicating whether to include internal standards (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

Median raw-signal abundance floor: drop features whose median feature_intensity across the selected QC types is below this value. NA (default) applies no threshold. Use to hide low-signal features.

min_correction_pct

Keep only features whose median correction (percent of raw signal removed, across the selected QC types) is at least this value. NA (default) applies no threshold. Use to focus the plot on substantially-corrected features.

sort_by_effect

Order the x-axis by correction effect, defined per feature as the deviation of its median % change from 100% (pooled across the displayed QC-type points). One of "none" (default, alphabetical), "desc" (largest effect first) or "asc".

top_n

Keep only the top_n features with the largest correction effect (see sort_by_effect). NA (default) keeps all. Applied after the min_median_value / min_correction_pct filters.

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_matrixeffects(), 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()