In airr-community/ogrdbstats: Analysis of Adaptive Immune Receptor Repertoire Germ Line Statistics

  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) {
        for (i in 1:length(end_composition_grobs)) {
            gridExtra::grid.arrange(grobs=end_composition_grobs[i],ncol=1)
        }
    }

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) {
        for (i in 1:length(cons_composition_grobs)) {
            gridExtra::grid.arrange(grobs=cons_composition_grobs[i],ncol=1)
        }
    }

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) {
        for (i in 1:length(triplet_composition_grobs)) {
            gridExtra::grid.arrange(grobs=triplet_composition_grobs[i],ncol=1)
        }
    }

CDR3 length distribution, in assignments to novel alleles

    if (length(cdr3_dist_grobs) > 0) {
      for (i in 1:length(cdr3_dist_grobs)) {
          gridExtra::grid.arrange(grobs=cdr3_dist_grobs[i],ncol=1)
      }
    }

\newpage

Variation from germline, in assignments to each allele

    if (length(barplot_grobs) > 0) {
      for (i in 1:length(barplot_grobs)) {
          gridExtra::grid.arrange(grobs=barplot_grobs[i],ncol=1)
      }
    }

\newpage

Allele usage in potential haplotype anchor genes

  gridExtra::grid.arrange(a_allele_plot, ncol=1)

\newpage

Haplotype plots

    if (length(haplo_grobs) > 0) {
      for (i in 1:length(haplo_grobs)) {
          gridExtra::grid.arrange(grobs=haplo_grobs[i],ncol=1)
      }
    }

\newpage

Configuration settings

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

airr-community/ogrdbstats documentation built on Feb. 17, 2025, 5:05 p.m.