write_plot_file {ogrdbstats}

Create the OGRDB style plot file

Description

Create the OGRDB style plot file

Usage

write_plot_file(
  filename,
  input_sequences,
  cdr3_dist_grobs,
  end_composition_grobs,
  cons_composition_grobs,
  whole_composition_grobs,
  triplet_composition_grobs,
  barplot_grobs,
  a_allele_plot,
  haplo_grobs,
  message,
  format
)

Arguments

filename

name of file to create (pdf)

input_sequences

the input_sequences data frame

cdr3_dist_grobs

cdr3 length distribution grobs created by make_novel_base_grob

end_composition_grobs

end composition grobs created by make_novel_base_grobs

cons_composition_grobs

consensus composition grobs created by make_novel_base_grobs

whole_composition_grobs

whole composition grobs created by make_novel_base_grobs

triplet_composition_grobs

triplet composition grobs created by make_novel_base_grobs

barplot_grobs

barplot grobs created by make_barplot_grons

a_allele_plot

a_allele_plot grob created by make_haplo_grobs

haplo_grobs

haplo_grobs created by make_haplo_grobs

message

text message to display at end of report

format

Format of report ('pdf', 'html' or 'none')

Value

None

Examples

plot_file = tempfile(pattern = 'ogrdb_plots')

base_grobs = make_novel_base_grobs(
                 example_rep$inferred_seqs,
                 example_rep$input_sequences,
                 'V',
                 FALSE
             )
barplot_grobs = make_barplot_grobs(
                      example_rep$input_sequences,
                      example_rep$genotype_db,
                      example_rep$inferred_seqs,
                      example_rep$genotype,
                      'V',
                      example_rep$calculated_NC
               )
haplo_grobs = make_haplo_grobs('V', example_rep$haplo_details)

write_plot_file(
    plot_file,
    example_rep$input_sequences,
    base_grobs$cdr3_dist,
    base_grobs$end,
    base_grobs$conc,
    base_grobs$whole,
    base_grobs$triplet,
    barplot_grobs,
    haplo_grobs$aplot,
    haplo_grobs$haplo,
    "Notes on this analysis",
    'none'
)

file.remove(plot_file)