Create HOPACH tree

Source: R/runHOPACH.R

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

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

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
#> Warning: Removed 4 rows containing missing values (geom_text).