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, merge_node = merge_node_param(),
        parent_node, top_n = NULL, top_value_method = object@list[[1]]@top_value_method,
        method = c("PCA", "MDS", "t-SNE", "UMAP"), color_by = NULL,
        scale_rows = object@list[[1]]@scale_rows, verbose = TRUE, ...)

### Arguments

`object` | A `HierarchicalPartition-class` object.
`merge_node` | Parameters to merge sub-dendrograms, see `merge_node_param`.
`top_n` | Top n rows to use. By default it uses all rows in the original matrix.
`top_value_method` | Which top-value method to use.
`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`.
`color_by` | If annotation table is set, an annotation name can be set here.
`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

    data(golub_cola_rh)
    dimension_reduction(golub_cola_rh)

[Package cola version 1.8.1 Index]