table.R

qc = read.table(file.path(path_results, "metrics", "metrics.tsv"),
                header=T, sep="\t", check.names=F,
                colClasses=list("sample"="character"))
rownames(qc) = qc$sample
qc$Mapped_reads_pct = as.numeric(gsub("%", "", qc$Mapped_reads_pct))
qc$Duplicates_pct = as.numeric(gsub("%", "", qc$Duplicates_pct))

metrics = c("sample", "Total_reads" ,"Mapped_reads_pct", "Duplicates_pct",
            "offtarget",
            "%GC", "Sequence_length", "Median_insert_size")

if (is.null(qc$offtarget)) {
  qc$offtarget <- rep  (0, length(qc$sample))
} else {
  qc$offtarget = qc$offtarget/qc$Total_reads
}

qc$Mapped_reads_pct <- qc$Mapped_reads_pct / 100
qc$Duplicates_pct <- qc$Duplicates_pct / 100

datatable(qc[, metrics],
          rownames=FALSE,
          options=list(dom = 't')) %>%
  formatPercentage('Mapped_reads_pct', 1) %>%
  formatPercentage('Duplicates_pct', 1) %>%
  formatPercentage('offtarget', 1)