printPCA {RiboProfiling} | R Documentation |
Plots the PCA scatterplots produced by codonPCA function.
printPCA(listPCAGraphs)
listPCAGraphs |
a list of 5 PCA ggplot scatterplots. |
a unique plot with the 5 PCA scatterplots.
#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]])