dimension_reduction-HierarchicalPartition-method: Visualize columns after dimension reduction

In cola: A Framework for Consensus Partitioning

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 <[e-mail]>

Examples

# There is no example
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cola documentation built on Nov. 8, 2020, 8:12 p.m.