runHOPACH: Create HOPACH tree

In SydneyBioX/scClassify: scClassify: single-cell Hierarchical Classification

Description

A function generating HOPACH tree using the average expression matrix for each cell type.

Usage

runHOPACH(data, plot = TRUE, kmax = 5)

Arguments

data	A matrix of average expression matrix (each row indicates the gene, each column indicates the cell type)
plot	Indicate whether plot or not
kmax	Integer between 1 and 9 specifying the maximum number of children at each node in the tree.

Value

Return a list where

• cutree_list: A list indicates the hierarchical cell type tree

• plot: A ggplot visualise the cell type tree

Author(s)

Yingxin Lin

References

van der Laan, M. J. and Pollard, K. S. (2003) ‘A new algorithm for hybrid hierarchical clustering with visualization and the bootstrap’, Journal of Statistical Planning and Inference. doi: 10.1016/S0378-3758(02)00388-9.

Examples

data("scClassify_example")
wang_cellTypes <- factor(scClassify_example$wang_cellTypes)
exprsMat_wang_subset <- scClassify_example$exprsMat_wang_subset
avgMat_wang <- apply(exprsMat_wang_subset, 1, function(x)
aggregate(x, list(wang_cellTypes), mean)$x)
rownames(avgMat_wang) <- levels(wang_cellTypes)
res_hopach <- runHOPACH(avgMat_wang)
res_hopach$plot

SydneyBioX/scClassify documentation built on Oct. 22, 2021, 4:03 p.m.