dimension_reduction-HierarchicalPartition-method {cola} | R Documentation

## Visualize columns after dimension reduction

### Description

Visualize columns after dimension reduction

### Usage

    ## S4 method for signature 'HierarchicalPartition'
    dimension_reduction(object,
        depth = max_depth(object), parent_node,
        top_n = NULL, method = c("PCA", "MDS", "t-SNE", "UMAP"),
        scale_rows = TRUE, verbose = TRUE, ...)

### Arguments

`object` | A `HierarchicalPartition-class` object.
`depth` | Depth of the hierarchy.
`top_n` | Top n rows to use. By default it uses all rows in the original matrix.
`parent_node` | Parent node. If it is set, the function call is identical to `dimension_reduction(object[parent_node])`
`method` | Which method to reduce the dimension of the data. `MDS` uses `cmdscale`, `PCA` uses `prcomp`. `t-SNE` uses `Rtsne`. `UMAP` uses `umap`.
`scale_rows` | Whether to perform scaling on matrix rows.
`verbose` | Whether print messages.
`...` | Other arguments passed to `dimension_reduction,ConsensusPartition-method`.

### Details

The class IDs are extract at `depth`.

### Value

No value is returned.

### Author(s)

Zuguang Gu <z.gu@dkfz.de>

### Examples

    # There is no example
    NULL

[Package cola version 1.6.0 Index]