dimension_reduction-matrix-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 'matrix'
dimension_reduction(object,
    pch = 16, col = "black", cex = 1, main = NULL,
    method = c("PCA", "MDS", "t-SNE", "UMAP"),
    pc = NULL, control = list(),
    scale_rows = FALSE, nr = 5000,
    internal = FALSE, verbose = TRUE)

Arguments

object	A numeric matrix.
method	Which method to reduce the dimension of the data. MDS uses cmdscale, PCA uses prcomp. t-SNE uses Rtsne. UMAP uses umap.
pc	Which two principle components to visualize
control	A list of parameters for Rtsne or umap.
pch	Ahape of points.
col	Color of points.
cex	Aize of points.
main	Title of the plot.
scale_rows	Whether perform scaling on matrix rows.
nr	If number of matrix rows is larger than this value, random nr rows are used.
internal	Internally used.
verbose	Whether print messages.

Value

Locations of the points.

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
NULL

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