createDimRedPlotData: Generate data for dimension reduction plot

In BIONF/PhyloProfile: PhyloProfile

Generate data for dimension reduction plot

Description

Generate data for dimension reduction plot

Usage

createDimRedPlotData(dimRedCoord = NULL, data4dimRed = NULL,
    freqCutoff = c(0,200), excludeTaxa = "None", currentNCBIinfo = NULL)

Arguments

dimRedCoord	data contains DIM reduction coordinates (from dimReduction)
data4dimRed	data for dimension reduction (from prepareDimRedData())
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

prepareDimRedData, dimReduction

Examples

rawInput <- system.file(
   "extdata", "test.main.long", package = "PhyloProfile", mustWork = TRUE
)
longDf <- createLongMatrix(rawInput)
data4dimRed <- prepareDimRedData(longDf, "phylum")
dimRedCoord <- dimReduction(data4dimRed)
createDimRedPlotData(dimRedCoord, data4dimRed)

BIONF/PhyloProfile documentation built on Dec. 18, 2024, 7:33 a.m.