cluster_k_sweep: Show the clustering at every k (see how it deteriorates)

In MosaiClusteR: An Umbrella Framework for Multi-Source and Multi-Omics Clustering

Show the clustering at every k (see how it deteriorates)

Description

Rather than only reporting the best k, project the objects to a fixed 2-D embedding and recolour them by the k-cut for each candidate k in a grid, annotating the average silhouette per panel. This makes it visible how the structure splits and degrades as k grows.

Usage

cluster_k_sweep(
  x,
  k_range = 2:6,
  linkage = "ward.D2",
  embed = c("pca", "umap", "tsne"),
  ncol = 3,
  point_size = 2.2,
  alpha = 0.9,
  palette = "Dark 3",
  base_size = 13
)

Arguments

x	A fitted result ($DistM), a dissimilarity, or a List.
k_range	Candidate cluster counts to display.
linkage	Agglomeration method used to cut the fused dissimilarity.
embed	Embedding for the (fixed) 2-D coordinates: "pca" (default), "umap" or "tsne".
ncol	Columns in the panel grid.
point_size	Diameter of the plotted points (default 2.2); raise it for larger, clearer markers.
alpha	Point opacity (default 0.9).
palette	Discrete hcl.colors palette used to colour the clusters (default "Dark 3").
base_size	Base font size passed to the ggplot2 theme.

Details

The panels are drawn with ggplot2 for a clean, high-resolution result whose quality is preserved when the figure is rescaled – save the returned object to a vector device (PDF/SVG) or a high-DPI raster for publication, e.g. ggplot2::ggsave("ksweep.pdf", cluster_k_sweep(fit), width = 9, height = 6).

Value

Invisibly the ggplot object (also printed, so it draws on an open device); the average silhouette per k is attached as the attribute "silhouette".

See Also

cluster_selection_plot, embedding_plot

Examples

data(mosaic_toy)
fit <- M_ABC(mosaic_toy$List, numsim = 40, NC = 3)
cluster_k_sweep(fit, k_range = 2:6, point_size = 3)

MosaiClusteR documentation built on Oct. 25, 2026, 1:08 a.m.