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 = 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 <z.gu@dkfz.de>

### Examples

    # There is no example
    NULL

[Package cola version 1.8.1 Index]