SampleTree.STACAS: Integration tree generation

In carmonalab/STACAS: STACAS: Sub-Type Anchoring Correction for Alignment in Seurat

Integration tree generation

Description

Build an integration tree by clustering samples in a hierarchical manner. Cumulative scoring among anchor pairs will be used as pairwise similarity criteria of samples.

Usage

SampleTree.STACAS(
  anchorset,
  obj.names = NULL,
  hclust.method = c("single", "complete", "ward.D2", "average"),
  usecol = c("score", "dist.mean"),
  method = c("weight.sum", "counts"),
  semisupervised = TRUE,
  plot = TRUE
)

Arguments

anchorset	Scored anchorsobtained from FindAnchors.STACAS and FilterAnchors.STACAS function
obj.names	Option vector of names for objects in anchorset
hclust.method	Clustering method to be used (single, complete, average, ward)
usecol	Column name to be used to compute sample similarity. Default "score"
method	Aggregation method to be used among anchors for sample similarity computation. Default: weight.sum
semisupervised	Whether to use cell type label information (if available)
plot	Logical indicating if dendrogram must be plotted

Value

An integration tree to be passed to the integration function.

carmonalab/STACAS documentation built on Feb. 3, 2024, 7:42 a.m.