https://github.com/arjunrajlaboratory/RajLabSeqTools
Tip revision: c8b8c79b2ec9c1bd9eb7ced427bb2aec25f19506 authored by Benjamin Emert on 26 March 2020, 17:37:11 UTC
Updated reorganizeBasespaceFiles.py to better parse samples with same first index (e.g. sample 1 and sample10)
Updated reorganizeBasespaceFiles.py to better parse samples with same first index (e.g. sample 1 and sample10)
Tip revision: c8b8c79
plot-pca.R
log <- file(snakemake@log[[1]], open="wt")
sink(log)
sink(log, type="message")
library("DESeq2")
# load deseq2 data
dds <- readRDS(snakemake@input[[1]])
# obtain normalized counts
counts <- rlog(dds, blind=FALSE)
svg(snakemake@output[[1]])
plotPCA(counts, intgroup=snakemake@params[["pca_labels"]])
dev.off()
