deriveHierarchy: Derive Hierarchy

In khodosevichlab/CellAnnotatoR: Automated marker-based cell type annotation

Derive Hierarchy

Description

derive hierarchy from the data using hclust

Usage

deriveHierarchy(feature.matrix, annotation, dist.method = "cor", max.depth = 2)

Arguments

feature.matrix	matrix where rows represent cells and columns represent either genes or some embedded space (e.g. PCA)
annotation	vector with cell type label per cell
dist.method	method for pairwise distance estimation. Either "cor" for correlation distance or any method supported by 'dist' function
max.depth	maximal depth of the hierarchy

Value

list with cell type hierarchy

Examples

  hierarchy <- deriveHierarchy(pca_mtx, annotation, max.depth=3)
  clf_tree <- hierarchyToClassificationTree(hierarchy)
  plotTypeHierarchy(clf_tree)

khodosevichlab/CellAnnotatoR documentation built on June 29, 2022, 9:12 p.m.