misc/demo.R

In neurogenomics/scFlowExamples: Provide example datsets to run scFlow

library(scFlowExamples)

write_data <- function(output_dir = ".") {

  # load data
  data("indvExp")

  # Create a folder to store the 10xGenomics matrix format data
  output_path <- file.path(output_dir, "tmp_Zeisel2015_scflow")
  dir.create(output_path)

  for (i in 1:length(indvExp)) {
    x <- indvExp[[i]]$exp

    # Convert gene symbols from mouse to human
    # Limit genes to Mouse:Human orthologs
    # Convert human gene symbols to Ensembl gene IDs

    x <- mouse_symbol_to_human_ensembl(x)

    # Write the data

    output_file <- sprintf("%s/individual_%s", output_path, i)
    DropletUtils::write10xCounts(output_file, x,
      barcodes = colnames(x),
      gene.id = rownames(x),
      gene.symbol = rownames(x),
      gene.type = "Gene Expression",
      overwrite = TRUE,
      type = "auto",
      genome = "unknown",
      version = "3"
    )
  }
}

write_scflow_manifest <- function(indvExp = indvExp, output_dir = ".") {

  output_path <- file.path(output_dir, "tmp_Zeisel2015_scflow")
  y <- ids::proquint(n = length(indvExp), n_words = 1L, use_cache = TRUE, use_openssl = FALSE)
  z <- data.frame(key = y, filepath = sprintf("%s/%s", output_path, list.files(output_path, pattern = "individual")), stringsAsFactors = FALSE)
  write.table(z, file = sprintf("%s/Manifest.txt", output_path), row.names = FALSE, col.names = TRUE, quote = FALSE, sep = "\t")
}


write_scflow_samplesheet <- function(indvExp = indvExp, output_dir = "."){

  output_path <- file.path(output_dir, "tmp_Zeisel2015_scflow")
  manifest <- read.delim(file = file.path(output_path, "Manifest.txt"), header = TRUE)
  dx <- unlist(lapply(indvExp, FUN = function(x) {
    return(x$dx)
  }))
  sex <- sample(c("M", "F"), length(dx), replace = T)
  age <- sample(1:100, length(dx))
  sample_sheet <- cbind(manifest = manifest$key, individual = rownames(manifest), diagnosis = dx, sex = sex)
  write.table(sample_sheet, file = sprintf("%s/SampleSheet.tsv", output_path), row.names = FALSE, col.names = TRUE, quote = FALSE, sep = "\t")
}


write_data()

write_scflow_manifest(indvExp)

write_scflow_samplesheet(indvExp)