Split Dendrogram

getDendrogramSplits()

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

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

Value

A data.table object

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 sub-dendrograms. This information can be used to determine in a hierarchical manner differentially expressed marker genes at each node.

Examples

if (FALSE) {
data("mini_giotto_single_cell")

splits = getDendrogramSplits(mini_giotto_single_cell, cluster_column = 'leiden_clus')
}