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"),
    silhouette_cutoff = 0.5, scale_rows = 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.

silhouette_cutoff

Cutoff of silhouette score. Data points with values less than it will be mapped to small points.

scale_rows

Whether perform scaling on matrix rows.

Details

The class IDs are extract at depth.

Value

No value is returned.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

data(cola_rh)
dimension_reduction(cola_rh)
dimension_reduction(cola_rh, parent_node = "00")

[Package cola version 1.0.1 Index]