groupLabelUmapData: Reduce the number of labels for UMAP plot based on the...

In BIONF/PhyloProfile: PhyloProfile

Reduce the number of labels for UMAP plot based on the gene/taxon frequency

Description

Reduce the number of labels for UMAP plot based on the gene/taxon frequency

Usage

groupLabelUmapData(data4umap = NULL, freqCutoff = c(0,200))

Arguments

data4umap	data for UMAP clustering (output from prepareUmapData)
freqCutoff	gene/taxon frequency cutoff range. Any labels that are outside of this range will be assigned as [Other]

Value

A dataframe similar to input data4umap, but with modified Label column, where less frequent labels are grouped together as "Other"

Author(s)

Vinh Tran [e-mail]

See Also

prepareUmapData

Examples

rawInput <- system.file(
   "extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE
)
longDf <- createLongMatrix(rawInput)
data4umap <- prepareUmapData(longDf, "phylum")
groupLabelUmapData(data4umap, freqCutoff = c(3,5))

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