decide_cluster_order: decide_cluster_order
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

decide_cluster_order

R Documentation

decide_cluster_order

Description

creates order for clusters

Usage

decide_cluster_order(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  feats,
  genes = NULL,
  cluster_column = NULL,
  cluster_order = c("size", "correlation", "custom"),
  cluster_custom_order = NULL,
  cor_method = "pearson",
  hclust_method = "ward.D"
)

Arguments

`gobject`	giotto object
`spat_unit`	spatial unit (e.g. "cell")
`feat_type`	feature type (e.g. "rna", "dna", "protein")
`expression_values`	expression values to use (e.g. "normalized", "scaled", "custom")
`feats`	features to use (e.g. genes)
`genes`	deprecated, use feats
`cluster_column`	name of column to use for clusters (e.g. "leiden_clus")
`cluster_order`	method to determine cluster order (e.g. "size", "correlation", "custom")
`cluster_custom_order`	custom order for clusters
`cor_method`	method for correlation, default to 'pearson'
`hclust_method`	method for hierarchical clustering, default to 'ward.D'