nice plot using ggplot2 from prcomp function

degPCA(counts, metadata = NULL, condition = NULL, pc1 = "PC1",
  pc2 = "PC2", name = NULL, shape = NULL)

Arguments

counts

matrix with count data

metadata

dara.frame with sample information

condition

character column in metadata to use to color samples

pc1

character PC to plot on x-axis

pc2

character PC to plot on y-axis

name

character if given, column in metadata to print label

shape

character if given, column in metadata to shape points

Examples

data(humanGender) library(DESeq2) idx <- c(1:10, 75:85) dse <- DESeqDataSetFromMatrix(assays(humanGender)[[1]][1:1000, idx], colData(humanGender)[idx,], design=~group) degPCA(log2(counts(dse)+0.5), colData(dse), condition="group", name="group", shape="group")