dimReduction: Perform dimension reduction 2D

In BIONF/PhyloProfile: PhyloProfile

Perform dimension reduction 2D

Description

Perform dimension reduction 2D

Usage

dimReduction(data4dimRed = NULL, by = "taxa", type = "binary",
    randomSeed = 123, reductionTechnique = "umap", dimension = "2d",
    tsneIter = 1000)

Arguments

data4dimRed	data for dimension reduction (from prepareDimRedData)
by	cluster data by "taxa" (default) or "genes"
type	type of data, either "binary" (default) or "non-binary"
randomSeed	random seed. Default: 123
reductionTechnique	dimensionality reduction technique, either "umap" (default) or "tsne"
dimension	either "2d" (default) or "3d"
tsneIter	number of iterations for t-SNE. Default: 1000

Value

A table contains coordinates of the 2D dimension reduction

Author(s)

Vinh Tran [e-mail]

See Also

prepareDimRedData

Examples

rawInput <- system.file(
   "extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE
)
longDf <- createLongMatrix(rawInput)
data4dimRed <- prepareDimRedData(longDf, "phylum")
dimReduction(data4dimRed)

BIONF/PhyloProfile documentation built on Dec. 23, 2024, 4:23 a.m.