Plot hex map of PlasmoMAPI output

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(),
  labeled_points = NULL,
  point_size = 1,
  point_colour = "white",
  point_fill = "black",
  point_stroke = 0.2,
  plot_data_values = FALSE
)

Arguments

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	optional list of polygon coordinates that are added to plot.
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.
plot_data_values	whether to plot aggregated data values instead of z-score, if available