draw 2D PCA from rld

library(ggplot2)
data <- plotPCA(rld, intgroup=c("condition", "donor"), returnData=TRUE)
ggplot(data, aes(x=PC1, y=PC2, color=condition, shape=donor)) +
      geom_point(size=8) + labs(x = "PC1", y = "PC2") +
      scale_color_manual(values = c("untreated" = "grey",
                                    "mCh d3"="#a6cee3",
                                    "mCh d8"="#1f78b4",
                                    "GFP+mCh d9/12"="cyan",
                                    "GFP d3"="#b2df8a",
                                    "GFP d8"="#33a02c",
                                    "sT d3"="#fb9a99",
                                    "sT d8"="#e31a1c",
                                    "LT d3"="#fdbf6f",
                                    "LT d8"="#ff7f00",
                                    "LTtr d3"="#cab2d6",
                                    "LTtr d8"="#6a3d9a",
                                    "sT+LT d3"="#ffff99",                        
                                    "sT+LTtr d9/12"="#a14a1a")) 
      xlab(paste0("PC1: ",percentVar[1],"% variance")) +
      ylab(paste0("PC2: ",percentVar[2],"% variance")) + theme(axis.text = element_text(face="bold",size = 21), axis.title = element_text(face="bold",size = 21)) + theme(legend.text = element_text(size = 20)) + theme(legend.title = element_text(size = 22)) + guides(color = guide_legend(override.aes = list(size = 10)), shape = guide_legend(override.aes = list(size = 10)), alpha = guide_legend(override.aes = list(size = 10)))

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