View source: R/umapClustering.R
prepareUmapData | R Documentation |
Prepare data for UMAP
prepareUmapData(longDf = NULL, taxonRank = NULL, type = "taxa",
taxDB = NULL, filterVar = "both", cutoff = 0)
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 |
A dataframe in wide format
Vinh Tran tran@bio.uni-frankfurt.de
rawInput <- system.file(
"extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE
)
longDf <- createLongMatrix(rawInput)
prepareUmapData(longDf, "phylum")
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