doHclust: doHclust

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

doHclust

Description

cluster cells using hierarchical clustering algorithm

Usage

doHclust(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  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("pearson", "spearman", "original", "euclidean", "maximum",
    "manhattan", "canberra", "binary", "minkowski"),
  agglomeration_method = c("ward.D2", "ward.D", "single", "complete", "average",
    "mcquitty", "median", "centroid"),
  k = 10,
  h = NULL,
  name = "hclust",
  return_gobject = TRUE,
  set_seed = T,
  seed_number = 1234
)

Arguments

gobject	giotto object
expression_values	expression values to use
genes_to_use	subset of genes to use
dim_reduction_to_use	dimension reduction to use
dim_reduction_name	dimensions reduction name
dimensions_to_use	dimensions to use
distance_method	distance method
agglomeration_method	agglomeration method for hclust
k	number of final clusters
h	cut hierarchical tree at height = h
name	name for hierarchical clustering
return_gobject	boolean: return giotto object (default = TRUE)
set_seed	set seed
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

hclust

Examples

data(mini_giotto_single_cell)

mini_giotto_single_cell = doHclust(mini_giotto_single_cell, k = 4, name = 'hier_clus')
plotUMAP_2D(mini_giotto_single_cell, cell_color = 'hier_clus', point_size = 3)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.