colour_acquired_amr_data — colour_acquired_amr

Takes a dataframe with acquired gene AMR prediction data and converts it into columms for microreact colouring

colour_acquired_amr_data(
  acquired_amr_data,
  id_cutoff = 90,
  cov_cutoff = 5,
  present_colour = "#ff6b6b",
  absent_colour = "#efefef",
  max_number_genes = 5
)

Arguments

acquired_amr_data	A dataframe of acquired gene AMR data where there are 4 columns for each gene. __assembled, __refseq, __pct_id, __ctg_cov
absent_color	the html colour to use when a gene is absent
absence_characters	the character to use when a gene is absent

Value

A dataframe where for each mutation there will be 2 columns. One with the gene name and a value of the refseq if the gene was present and '-' if absent. Another with the gene name and the suffix '__colour'. This will be 'red' or 'lime' if the gene was present or absent respectively