nice plot using ggplot2 from prcomp function

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

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

data

Whether return PCA data or just plot the PCA.

Value

if results <- used, the function return the output of prcomp().

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")