Visualize columns after dimension reduction

# S4 method for 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

Zuguang Gu <z.gu@dkfz.de>

Examples

# There is no example
NULL
#> NULL