getDendrogramSplits: getDendrogramSplits

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

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

Usage

getDendrogramSplits(
  gobject,
  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

gobject	giotto object
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

Examples

    getDendrogramSplits(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.