printPCA: Plots the PCA scatterplots produced by codonPCA function.

In RiboProfiling: Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

Description

Plots the PCA scatterplots produced by codonPCA function.

Usage

printPCA(listPCAGraphs)

Arguments

listPCAGraphs

a list of 5 PCA ggplot scatterplots.

Value

a unique plot with the 5 PCA scatterplots.

Examples

#How to perform a PCA analysis based on codon coverage
data(codonDataCtrl)
codonData <- codonDataCtrl
codonUsage <- codonData[[1]]
codonCovMatrix <- codonData[[2]]

#keep only genes with a minimum number of reads
nbrReadsGene <- apply(codonCovMatrix, 1, sum)
ixExpGenes <- which(nbrReadsGene >= 50)
codonCovMatrix <- codonCovMatrix[ixExpGenes, ]

#get the PCA on the codon coverage
codonCovMatrixTransp <- t(codonCovMatrix)
rownames(codonCovMatrixTransp) <- colnames(codonCovMatrix)
colnames(codonCovMatrixTransp) <- rownames(codonCovMatrix)

listPCACodonCoverage <- codonPCA(codonCovMatrixTransp,"codonCoverage")
printPCA(listPCACodonCoverage[[2]])

RiboProfiling documentation built on Nov. 8, 2020, 5:26 p.m.