UMAP with Pie Charts at Cluster Centroids

Overlays proportional pie charts on a UMAP (or any 2D reduction) - one pie per level of group.by - where each slice shows the fraction of cells from each level of split.by (e.g. sample composition per cluster).

Uses ggforce::geom_arc_bar for stable pie rendering that works correctly with ggplot2 >= 3.4 (unlike the old coord_polar approach).

Usage

PlotPieUMAP(
  seurat_object,
  group.by,
  split.by,
  reduction = "umap",
  pie_scale = 1,
  bg_color = "lightgray",
  bg_alpha = 0.3,
  pt.size = 0.4,
  split_colors = NULL,
  label = TRUE,
  label_size = 3,
  output_dir = NULL,
  object_name = "",
  subset_name = "",
  file_name = NULL,
  width = NULL,
  height = NULL,
  timestamp = FALSE
)

Arguments

seurat_object

A Seurat object.

group.by

Metadata column defining the groups/clusters. One pie chart is placed at each group's centroid in the reduction space.

split.by

Metadata column whose level proportions define the pie slices (e.g. "Sample" shows how much of each cluster is each sample).

reduction

Dimensionality reduction to use. Default "umap".

pie_scale

Scaling multiplier for pie radius (1 = auto-sized). Increase for larger pies, decrease if pies overlap. Default 1.

bg_color

Background scatter point color. Default "lightgray".

bg_alpha

Background scatter point transparency. Default 0.3.

pt.size

Background scatter point size. Default 0.4.

split_colors

Named character vector of colors for split.by levels. Auto-assigned from PrepObject or Nour_pal if NULL.

label

Logical. Add cluster labels at centroids. Default TRUE.

label_size

Font size for cluster labels. Default 3.

output_dir

Directory to save a PDF. NULL = no save.

object_name

Label prefix for output file names.

subset_name

Optional subset label.

file_name

Character or NULL. Base name (no extension) for the saved PDF. NULL (default) auto-deduces from object_name, subset_name, group.by, and split.by.

width, height

Numeric or NULL. Override the auto-calculated PDF dimensions in inches. NULL (default) uses a fixed 7 x 6 in panel.

timestamp

Logical. When TRUE, append a _YYYYMMDD-HHMMSS stamp to the saved file name so repeated runs are versioned instead of overwriting the previous PDF. Default FALSE.

Value

A ggplot2 object.