printPCA {RiboProfiling} | R Documentation

## Plots the PCA scatterplots produced by codonPCA function.

### 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]])

[Package RiboProfiling version 1.18.0 Index]