OGRDBstats Report

  arrange_cols = function(grobs, cols) {
      for (i in 1:length(grobs)/cols) {
        j = 1 + (i-1) * cols
        l = grobs[j:j+cols-1]
        l = l[!is.na(l)]

        if (length(l) > 0) {
            gridExtra::grid.arrange(grobs=l,ncol=cols)
        }
      }     
  }

\newpage

r if('SEQUENCE_IMGT' %in% names(input_sequences)){"# Novel sequence analysis"}

r if('SEQUENCE_IMGT' %in% names(input_sequences) && length(end_composition_grobs) > 0) {"## End-nucleotide composition"}

    if('SEQUENCE_IMGT' %in% names(input_sequences) && length(end_composition_grobs) > 0) {
      arrange_cols(end_composition_grobs, 2)
    }

r if('SEQUENCE_IMGT' %in% names(input_sequences) && length(cons_composition_grobs) > 0) {"## Per-nucleotide consensus where previous nucleotides match the consensus"}

    if('SEQUENCE_IMGT' %in% names(input_sequences) && length(cons_composition_grobs) > 0) {
      arrange_cols(cons_composition_grobs, 2)
    }

r if('SEQUENCE_IMGT' %in% names(input_sequences) && length(whole_composition_grobs) > 0) {"## Whole-sequence composition of each assigned read"}

    if('SEQUENCE_IMGT' %in% names(input_sequences) && length(whole_composition_grobs) > 0) {
      arrange_cols(whole_composition_grobs, 1)
    }

r if('SEQUENCE_IMGT' %in% names(input_sequences) && length(triplet_composition_grobs) > 0) {"## Final three nucleotides: frequency of each observed triplet"}

    if('SEQUENCE_IMGT' %in% names(input_sequences) && length(triplet_composition_grobs) > 0) {
      arrange_cols(triplet_composition_grobs, 2)
    }

CDR3 length distribution, in assignments to novel alleles

    arrange_cols(cdr3_dist_grobs, 3)

\newpage

Variation from germline, in assignments to each allele

    arrange_cols(barplot_grobs, 3)

\newpage

Allele usage in potential haplotype anchor genes

    arrange_cols(haplo_grobs, 1)

\newpage

Configuration settings

    m = gsub("\\\\", "/", message)
  cat(gsub("([*+-])", " ", m))


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ogrdbstats documentation built on March 31, 2023, 9:55 p.m.