doKmeans: doKmeans

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

doKmeans

Description

cluster cells using kmeans algorithm

Usage

doKmeans(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  feats_to_use = NULL,
  genes_to_use = NULL,
  dim_reduction_to_use = c("cells", "pca", "umap", "tsne"),
  dim_reduction_name = "pca",
  dimensions_to_use = 1:10,
  distance_method = c("original", "pearson", "spearman", "euclidean", "maximum",
    "manhattan", "canberra", "binary", "minkowski"),
  centers = 10,
  iter_max = 100,
  nstart = 1000,
  algorithm = "Hartigan-Wong",
  name = "kmeans",
  return_gobject = TRUE,
  set_seed = TRUE,
  seed_number = 1234
)

Arguments

gobject	giotto object
feat_type	feature type (e.g. "cell")
spat_unit	spatial unit (e.g. "rna", "dna", "protein")
expression_values	expression values to use (e.g. "normalized", "scaled", "custom")
feats_to_use	subset of features to use
genes_to_use	deprecated use feats_to_use
dim_reduction_to_use	dimension reduction to use (e.g. "cells", "pca", "umap", "tsne")
dim_reduction_name	dimensions reduction name, default to "pca"
dimensions_to_use	dimensions to use, default = 1:10
distance_method	distance method (e.g. "original", "pearson", "spearman", "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski")
centers	number of final clusters, default = 10
iter_max	kmeans maximum iterations, default = 100
nstart	kmeans nstart, default = 1000
algorithm	kmeans algorithm, default to "Hartigan-Wong"
name	name for kmeans clustering, default to "kmeans"
return_gobject	boolean: return giotto object (default = TRUE)
set_seed	set seed (default = TRUE)
seed_number	number for seed

Details

Description on how to use Kmeans clustering method.

Value

giotto object with new clusters appended to cell metadata

See Also

kmeans

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.