plotUmap: Create UMAP cluster plot

In BIONF/PhyloProfile: PhyloProfile

Create UMAP cluster plot

Description

Create UMAP cluster plot

Usage

plotUmap(plotDf = NULL, legendPos = "bottom", colorPalette = "Set2", 
    transparent = 0, textSize = 12, font = "Arial", highlightTaxa = NULL,
    dotZoom = 0)

Arguments

plotDf	data for UMAP plot
legendPos	position of legend. Default: "right"
colorPalette	color palette. Default: "Set2"
transparent	transparent level (from 0 to 1). Default: 0
textSize	size of axis and legend text. Default: 12
font	font of text. Default = Arial"
highlightTaxa	list of taxa to be highlighted
dotZoom	dot size zooming factor. Default: 0

Value

A plot as ggplot object

Author(s)

Vinh Tran [e-mail]

See Also

prepareUmapData, umapClustering, createUmapPlotData

Examples

rawInput <- system.file(
   "extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE
)
longDf <- createLongMatrix(rawInput)
umapData <- prepareUmapData(longDf, "phylum")
data.umap <- umapClustering(umapData)
plotDf <- createUmapPlotData(data.umap, umapData)
plotUmap(plotDf, font = "sans")

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