decide_cluster_order: decide_cluster_order

View source: R/auxiliary_visuals.R

decide_cluster_orderR 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'

Details

Calculates order for clusters.

Value

custom


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