Hi,

I'm wondering, how can you change the order in the PCA plot labeling:

I have "day0", "day1, "day2", "day8" and "day15", and by default, it puts "day15" before "day2" because of the alphabetical/numerical order. How can I fix it, so that "day15" comes at last?

plotPCA(vsd, intgroup="condition")
#
# levels(condition) gives
#[1] "day0"  "day1"  "day2"  "day8"  "day15"
# so, the order is correct here.

Thank you.

You have to change the factor levels in the vsd object itself, so vsd$condition <- factor(as.character(vsd$condition), levels=c("day0", "day1", "day2", "day8", "day15")).

Example:

library(DESeq2)

dds <- makeExampleDESeqDataSet()
vsd <- vst(dds, nsub=3)

vsd$condition <- relevel(vsd$condition, ref = "B")
plotPCA(vsd, "condition")