dimensionReduction: Dimensionality reduction with dimensionReduction methods PCA,...

In tnaake/MatrixQCvis: Shiny-based interactive data-quality exploration for omics data

Dimensionality reduction with dimensionReduction methods PCA, PCoA, NMDS, UMAP and tSNE

Description

The function dimensionReduction creates a data.frame with the coordinates of the projected data (first entry of returned output). The function allows for the following projections: Principal Component Analysis (PCA), Principal Coordinates Analysis/Multidimensional Scaling (PCoA), Non-metric Multidimensional scaling (NMDS), t-distributed stochastic neighbor embedding (tSNE), and Uniform Manifold Approximation and Projection (UMAP).

The second list entry will contains the object returned from prcomp (PCA), cmdscale (PCoA), isoMDS (NMDS), Rtsne (tSNE), or umap (UMAP).

Usage

dimensionReduction(
  x,
  type = c("PCA", "PCoA", "NMDS", "tSNE", "UMAP"),
  params = list()
)

Arguments

x	matrix, containing no missing values, samples are in columns and features are in rows
type	character, specifying the type/method to use for dimensionality reduction. One of PCA, PCoA, NMDS, tSNE, or UMAP.
params	list, arguments/parameters given to the functions stats::prcomp, stats::dist, Rtsne::Rtsne, umap::umap

Details

The function dimensionReduction is a wrapper around the following functions stats::prcomp (PCA), stats::cmdscale (PCoA), MASS::isoMDS (NMDS), Rtsne::Rtsne (tSNE), and umap::umap (UMAP). For the function umap::umap the method is set to naive.

Value

list, first entry contains a tbl, second entry contains the object returned from prcomp (PCA), cmdscale (PCoA), isoMDS (NMDS), Rtsne (tSNE), or umap (UMAP)

Author(s)

Thomas Naake

Examples

x <- matrix(rnorm(seq_len(10000)), ncol = 100)
rownames(x) <- paste("feature", seq_len(nrow(x)))
colnames(x) <- paste("sample", seq_len(ncol(x)))
params <- list(method = "euclidean", ## dist
    initial_dims = 10, max_iter = 100, dims = 3, perplexity = 3, ## tSNE
    min_dist = 0.1, n_neighbors = 15, spread = 1) ## UMAP
dimensionReduction(x, type = "PCA", params = params)
dimensionReduction(x, type = "PCoA", params = params)
dimensionReduction(x, type = "NMDS", params = params)
dimensionReduction(x, type = "tSNE", params = params)
dimensionReduction(x, type = "UMAP", params = params)

tnaake/MatrixQCvis documentation built on Nov. 4, 2024, 7:42 a.m.