AbundPcaPlot: Function to generate PCA plot of abundance table :...

In bmhoan/MMDR: Analysis of OTU and Functional 16S data

Description

Function to generate PCA plot of abundance table : OTU,GENE,KO

Usage

AbundPcaPlot(abund.tab, sp.meta, meanCountCutOff = 1, groups = "ALL",
  title = "Title")

Arguments

abund.tab	otu/gene table as matrix
sp.meta	sample metadata as.matrix (ID,NICKNAME,CONDITION,SUBJECT,CATEGORY)
meanCountCutOff	The mean count value a gene/otu must have to be considered for the plot.
groups	list of selected biological condition for plot

Value

PCA plot

Examples

AbundPcaPlot(OTUDATA$otu.tab,OTUDATA$sp.meta,groups=c('ain','protein','cholic'))
AbundPcaPlot(OTUDATA$otu.tab,OTUDATA$sp.meta,groups=c('protein','cholic'))
AbundPcaPlot(KODATA$ko.tab,OTUDATA$sp.meta,groups=c('protein','cholic'))

bmhoan/MMDR documentation built on July 4, 2019, 4:37 p.m.