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Example

example.Rmd

Example using default bayesian method on example file: 

  results = estimate_genome_size(example_input_file, sep='\t', match_column='TAXID', output_format='input', ci_threshold = 0.3)
  
  #############################################################################
  # Genome size estimation summary:
  #
  #  22.22222 % estimations achieving required precision
  #
       Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
    3007721   5408472  16980834  23969767  41811396 143278734 
  
  # Estimation status:
  Confidence interval to estimated size ratio > ci_threshold                                                         OK 
                                                         140                                                         40

Plot genome size histogram per sample: 

  plotted_df = plot_genome_size_histogram(results)

Plot genome size histogram for one sample: 

  plotted_df = plot_genome_size_histogram(results, only_sample='16S_1')

Plot genome size boxplot per sample: 

  plotted_df = plot_genome_size_boxplot(results)

Plot genome size boxplot for one sample: 

  plotted_df = plot_genome_size_boxplot(results, only_sample='ITS_1')

Plot simplified taxonomic tree with colour-coded estimated genome sizes: 

  plotted_df = plot_genome_size_tree(results, refdata_archive_path)
## Untarring reference data
## Using reference data in: /tmp/RtmpGgcSxU/refdata
## Untarring taxonomy
## Using taxonomy: /tmp/RtmpGgcSxU/taxdump