For RNASeq analysis, I am generating a PCA plot for various strains with three biological replicates each. When I make the PCA plot , I get a symbol on the plot for every replicate. For a large dataset, I was wondering if there is a way to have a single symbol (average of three biological replicates) be represented on the plot, instead of all three replicates.
In DESeq2 package I use:
data <- plotPCA(rld, intgroup=c("clade", "strain"), returnData=TRUE)
percentVar <- round(100 * attr(data, "percentVar"))
ggplot(data, aes(PC1, PC2, color=strain, shape=clade)) +
xlab(paste0("PC1: ",percentVar,"% variance")) +
ylab(paste0("PC2: ",percentVar,"% variance")) +