dimension_reduction-HierarchicalPartition-method: Visualize columns after dimension reduction

In jokergoo/cola: A Framework for Consensus Partitioning

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 <[e-mail]>

Examples

data(golub_cola_rh)
dimension_reduction(golub_cola_rh)

jokergoo/cola documentation built on Feb. 29, 2024, 1:41 a.m.