getDendrogramSplits#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/clustering.R#L2475

Description#

Split dendrogram at each node and keep the leave (label) information..

Usage#

getDendrogramSplits(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  cluster_column,
  cor = c("pearson", "spearman"),
  distance = "ward.D",
  h = NULL,
  h_color = "red",
  show_dend = TRUE,
  verbose = TRUE
)

Arguments#

Argument

Description

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

expression_values

expression values to use

cluster_column

name of column to use for clusters

cor

correlation score to calculate distance

distance

distance method to use for hierarchical clustering

h

height of horizontal lines to plot

h_color

color of horizontal lines

show_dend

show dendrogram

verbose

be verbose

Details#

Creates a data.table with three columns and each row represents a node in the dendrogram. For each node the height of the node is given together with the two subdendrograms. This information can be used to determine in a hierarchical manner differentially expressed marker genes at each node.

Value#

data.table object