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