doKmeans#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/clustering.R#L727

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#

Argument

Description

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

Seealso#

`kmeans <#kmeans>`__