kmeans_segmentation: kmeans segmentation function

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

kmeans segmentation function

Description

kmeans segmentation function

Usage

kmeans_segmentation(
  vesalius_assay,
  dimensions = seq(1, 3),
  col_resolution = 10,
  embedding = "last",
  verbose = TRUE
)

Arguments

vesalius_assay	a vesalius_assay
dimensions	numeric vector of latent space dimensions to use.
col_resolution	integer or vector of positive integers. Colour depth used for segmentation.
embedding	character string describing which embedding should be used.
verbose	logical - progress message output.

Details

Run an interaive kmeans segmentation with the possibility to run multiple rounds of smoothing.

Value

list containing segmented image as an active embedding and territory cluster for all barcodes.

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.