plot_map: Plot hex map of PlasmoMAPI output
In mrc-ide/PlasmoMAPI: Mapping Plasmodium Spatial Connectivity from Genetic Data

Plot hex map of PlasmoMAPI output.

plot_map(
  proj,
  col_scale = viridisLite::magma(100),
  plot_sampling_points = TRUE,
  plot_hex_grid = TRUE,
  min_hex_coverage = 10,
  plot_significance = TRUE,
  empirical_tail = "both",
  FDR = 0.05,
  zlim = NULL,
  base_plot = NULL,
  poly_list = list(),
  poly_col = "white",
  labeled_points = NULL,
  point_size = 1,
  point_colour = "white",
  point_fill = "black",
  point_stroke = 0.2
)

`proj`	object of class `pm_project`.
`col_scale`	the colour scale to use.
`plot_sampling_points`	whether to overlay sampling locations.
`plot_hex_grid`	whether to plot the hex map. If the project contains output then hexes will be coloured based on z-scores, otherwise a flat colour scheme will be used.
`min_hex_coverage`	minimum coverage (number of edges assigned to a hex) for it to be included in the final result, otherwise these hexes are given the value `NA`.
`plot_significance`	whether to outline areas that were identified as significant outliers.
`empirical_tail`	if plotting significance, whether to calculate empirical p-values using a one-sided test (`empirical_tail = "left"` or `empirical_tail = "right"`) or a two-sided test (`empirical_tail = "both"`).
`FDR`	the false discovery rate, i.e. the probability that a hex identified as significant is actually a false positive.
`zlim`	the limits of the colour scale. If `NULL` then these limits are chosen automatically.
`base_plot`	optional base plot (object of class `ggplot`) on which this function builds. If `NULL` then a simple empty plot is used.
`poly_list, poly_col`	optional list of polygon coordinates that are added to plot, and associated plotting parameters.
`labeled_points`	optional data frame of labeled points to add to graph.
`point_size, point_colour, point_fill, point_stroke`	properties of plotted sampling points.