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Plot QC filtering summary by feature class

Source: R/plots-qc-filtering.R
plot_qc_summary_byclass.Rd

This function provides a summary of feature QC filtering based on feature class, showing the number of features that passed or failed various quality control criteria. It visualizes the filtering in a hierarchical sequence. Features are first evaluated against lower-level filters such as signal-to-blank (S/B) ratios and limit of detection (LOD), followed by higher-level filters like the coefficient of variation (CV) or linear regression results. This means that a feature is classified as failing a given criterion (e.g., CV) only if it has passed all hierarchically lower filters (e.g., S/B ratio and LOD).

Usage

plot_qc_summary_byclass(
  data = NULL,
  font_base_size = NULL,
  legend_position = NULL,
  legend_size = NULL,
  show_legend_title = NULL,
  title = NULL
)

Arguments

data

A MRMhubExperiment object.

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.

Value

A ggplot object showing the feature QC filtering summary by feature class.

See also

plot_qc_summary_overall() for an overall summary plot filter_features_qc() for comparing QC metrics

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