Generate and Save Diversity Pie Charts

Creates pie charts visualising allele or haplotype diversity, pooling Day 0 and recurrence samples: one figure for all sites combined and one figure per site (when a Site column is present). Pies are arranged with at most max_cols per row.

Usage

plot_markers_diversity(
  genotypedata,
  data_type,
  marker_info = NULL,
  output_folder = NULL,
  filename_prefix = "diversity",
  max_cols = 4
)

Arguments

genotypedata

A dataframe containing the genotyping data.

data_type

A string: "length_polymorphic" or "ampseq".

marker_info

A dataframe with marker definitions; required when data_type = "length_polymorphic".

output_folder

Path to the directory where the output PNGs will be saved: <prefix>_<data_type>_comparison.png for all sites and <prefix>_<data_type>_<site>.png per site. If NULL, nothing is saved.

filename_prefix

A string prefix for the output filenames.

max_cols

Maximum number of pie charts per row. Defaults to 4.

Value

Invisibly returns a list with all_sites (one figure pooling all sites) and by_site (a list of figures named by site; NULL if there is no Site column), or NULL if no data.

Examples

if (FALSE) { # \dontrun{
  gdata <- data.frame(
    Sample.ID     = c("P1 Day 0", "P1 recurrence", "P2 Day 0", "P2 recurrence"),
    Site          = "SiteA",
    cpmp_allele_1 = c("HAPL_A", "HAPL_A", "HAPL_A", "HAPL_B"),
    cpmp_allele_2 = c(NA, NA, NA, NA)
  )
  plot_markers_diversity(genotypedata = gdata, data_type = "ampseq")
} # }