Mirror EIC comparison grid for feature groups — plot_xcms_feature_group_EIC

Pairwise chromatogram comparison for features in one or more xcms feature groups on an XcmsExperiment (or compatible) object. Panel $(i,j)$ shows the column feature EIC above $y = 0$ and the row feature EIC below (each cropped to its peak RT window via XChromatograms_subset_feature, exactly as the EIC grouping does, then normalized to its own max). Cell labels are EIC similarities from MsExperiment::otherData(xcms)$EIC_Similarity when available (e.g. after xcms_group_feature_EIC). Strip backgrounds are colored by feature group when ggh4x is installed.

Usage

plot_xcms_feature_group_EIC_comparasion(
  xcms,
  feature_group,
  chroms = NULL,
  expandRt = 2,
  min_width = 20,
  max_features = NULL,
  sample_index = 1L,
  title = NULL
)

Arguments

xcms: An XcmsExperiment / MsExperiment (or XCMSnExp) with feature definitions and featureGroups.
feature_group: Character vector of feature group id(s) to compare.
chroms: Optional XChromatograms for the features (rownames = feature ids) with a featureDefinitions slot carrying peakRtMin/peakRtMax. If NULL, extracted via get_xcms_feature_chromatogram.
expandRt: numeric(1). Seconds added on each side of each feature's [peakRtMin, peakRtMax] window when cropping via XChromatograms_subset_feature (default 2).
min_width: numeric(1). Minimum RT window width (seconds) after expandRt; shorter windows are padded equally on both sides (default 20).
max_features: Maximum features kept per group (ordered by rtmed). NULL keeps all members (default).
sample_index: Sample index into otherData(xcms)$EIC_Similarity when several samples are stored (default 1L).
title: Optional plot title. Default is "Feature group: <id> (<rt center>), ...", where the RT center is the median rtmed of each group's member features.

Value

A ggplot object.