runHOPACH {scClassify} | R Documentation

## Create HOPACH tree

### 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

[Package scClassify version 1.4.0 Index]