A function to wrap up the DESeq2 inputs&outputs, and plug that as SingleCellExperiment into iSEE

iSEE_plug.R

library(DESeq2)

wrapup_for_iSEE <- function(dds, res) {
  # dds to vst
  vst <- vst(dds)
  
  # initialize the container
  se <- SummarizedExperiment(
    assays = List(
      counts = counts(dds),
      normcounts = counts(dds,normalized = TRUE),
      vst_counts = assay(vst)
    )
  )
  
  # adding colData, taken directly from the DESeqDataSet object
  colData(se) <- colData(dds)
  
  # extract contrast info
  this_contrast <- sub(".*p-value: (.*)","\\1",mcols(res, use.names=TRUE)["pvalue","description"])
  
  # getting the rowData from the dds itself
  rdd <- rowData(dds)
  
  # modifying in advance the DESeqResults object
  res$log10_baseMean <- log10(res$baseMean)
  res$log10_pvalue <- -log10(res$pvalue)
  # and for the rowData
  rdd$log10_dispersion <- log10(rdd$dispersion)
  
  # adding rowData to se
  rowData(se)[[paste0("DESeq2_",gsub(" ","_",this_contrast))]] <- res
  
  # merging in the existing rowData slot
  rowData(se) <- cbind(rowData(se), rdd)
  
  return(se)
}

# next, launch iSEE directly on the se object!
se <- wrapup_for_iSEE(dds,res)
library(iSEE)
iSEE(se)