createUmapPlotData: Create UMAP cluster plot

In BIONF/PhyloProfile: PhyloProfile

Create UMAP cluster plot

Description

Create UMAP cluster plot

Usage

createUmapPlotData(umapData = NULL, data4umap = NULL, 
    freqCutoff = c(0,200), excludeTaxa = "None", currentNCBIinfo = NULL)

Arguments

umapData	data contains UMAP cluster (output from umapClustering())
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]
excludeTaxa	hide taxa from plot. Default: "None"
currentNCBIinfo	table/dataframe of the pre-processed NCBI taxonomy data (/PhyloProfile/data/preProcessedTaxonomy.txt)

Value

A plot as ggplot object

Author(s)

Vinh Tran [e-mail]

See Also

prepareUmapData, umapClustering

Examples

rawInput <- system.file(
   "extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE
)
longDf <- createLongMatrix(rawInput)
data4umap <- prepareUmapData(longDf, "phylum")
umapData <- umapClustering(data4umap)
createUmapPlotData(umapData, data4umap)

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