Heatmap of xcms feature-group EIC similarity — plot_xcms_feature_group

Draws the EIC similarity matrix produced by MSdev_group_feature_EIC / xcms_group_feature_EIC (stored on the xcms object at MsExperiment::otherData(xcms)$EIC_Similarity) as a ComplexHeatmap. Rows/columns are ordered either by rtmed (order_by = "rtmed") or by feature group (order_by = "feature_group": groups sorted by each group's median rtmed, features within a group by rtmed). The stored matrix is sparse: only compared pairs (within rt_tol) carry a score, so absent (uncompared) entries are densified to NA and shown in na_col (grey), while a genuine zero correlation stays on the ramp (white). A top color bar encodes rtmed (plus a feature-group bar when groups exist).

Usage

plot_xcms_feature_group_similarity(
  xcms,
  order_by = c("rtmed", "feature_group"),
  sample = 1L,
  rt_window = NULL,
  na_col = "#BDBDBD",
  box_top_n = 10L
)

Arguments

xcms: An xcms object (XcmsExperiment / XCMSnExp) that carries feature definitions, featureGroups, and an EIC_Similarity entry (e.g. ms@xcmsData$PositiveMS1).
order_by: "rtmed" (default) or "feature_group".
sample: Sample name or index selecting the per-sample similarity matrix (default first sample).
rt_window: Optional half-width (seconds) of a fixed RT window centered on the densest RT region, keeping the diagonal band visible. NULL (default) keeps all features.
na_col: Color for uncompared (NA) cells (default "#BDBDBD", grey).
box_top_n: Number of largest feature groups to outline with a box on the diagonal. Only applies to order_by = "feature_group" (where each group is a contiguous block). Set 0 / NULL to disable (default 10).

Value

(Invisibly) a ComplexHeatmap::Heatmap object.