Heatmap of MEM scores — mem

Visualizes MEM enrichment scores as a heatmap.

Usage

mem_heatmap(
  x,
  show_mem_labels = FALSE,
  min_label_score = 1,
  max_label_markers = 5,
  show_label_scores = FALSE,
  min_heatmap_score = 0,
  filename = NULL,
  width = 15,
  height = 8,
  cluster_rows = TRUE,
  cluster_columns = TRUE,
  ...
)

Arguments

x: The return value of altmem() or cytoMEM::MEM().
show_mem_labels: Whether to annotate rows with MEM labels. When TRUE, labels are generated via mem_labels() using min_label_score, max_label_markers, and show_label_scores. Defaults to FALSE.
min_label_score: Minimum absolute MEM score for a marker to be included in the label. Defaults to 1.
max_label_markers: Maximum number of markers to include per direction (positive and negative) in each label. Defaults to 5.
show_label_scores: Whether to include MEM scores alongside marker names in the MEM labels. Defaults to FALSE.
min_heatmap_score: Minimum absolute MEM score across any cluster for a marker to be shown as a column in the heatmap. Increase this to remove low variance markers. Defaults to 0 (show all markers).
filename: Optional file path to save the heatmap. The format is inferred from the extension (e.g., ".png", ".pdf", ".svg"). Defaults to NULL (no file saved).
width, height: Plot dimensions in inches. Only used when filename is provided.
cluster_rows: Whether to cluster rows. Defaults to TRUE.
cluster_columns: Whether to cluster columns. Defaults to TRUE.
...: Additional arguments passed to ComplexHeatmap::Heatmap().

Value

A ComplexHeatmap::Heatmap object, invisibly.