prepareUmapData: Prepare data for UMAP

In BIONF/PhyloProfile: PhyloProfile

Prepare data for UMAP

Description

Prepare data for UMAP

Usage

prepareUmapData(longDf = NULL, taxonRank = NULL, type = "taxa", 
    taxDB = NULL, filterVar = "both", cutoff = 0, groupLabelsBy = "taxa")

Arguments

longDf	input phyloprofile file in long format
taxonRank	taxonomy rank for labels (e.g. "phylum")
type	type of clustering, either "taxa" (default) or "genes"
taxDB	path to taxonomy database
filterVar	choose variable (either "var1", "var2" or "both") to filter the data. Default: "both"
cutoff	cutoff to filter data values. Default: 0
groupLabelsBy	group labels by the number of "taxa" (default) or "genes"

Value

A dataframe in wide format

Author(s)

Vinh Tran [e-mail]

Examples

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

BIONF/PhyloProfile documentation built on Nov. 7, 2024, 8:31 p.m.