Visualize columns after dimension reduction

# S4 method for 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

Zuguang Gu <z.gu@dkfz.de>

Examples

data(golub_cola_rh)
dimension_reduction(golub_cola_rh)
#> use UMAP