dimension_reduction-matrix-method {cola}R Documentation

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 = "",
    method = c("PCA", "MDS", "t-SNE", "UMAP"),
    pc = 1:2, control = list(),
    scale_rows = TRUE,
    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.

internal

Internally used.

verbose

Whether print messages.

Value

No value is returned.

Author(s)

Zuguang Gu <z.gu@dkfz.de>

Examples

# There is no example
NULL


[Package cola version 1.0.1 Index]