Create a standalone legend for trace phylogeny plots — plot_trace_phylo

Generates a combined legend plot for trace locations, surveillance results, and patient categories that can be saved separately from the main plot.

Usage

plot_trace_phylo_legend(
  trace_colors = trace_color_palette(),
  trace_labels = NULL,
  surv_colors = surv_dot_colors(),
  surv_shapes = surv_dot_shapes(),
  label_colors = c(index = "red", `multiply-colonized-index` = "darkred", `weak-index` =
    "orange", convert = "black", `adm-pos` = "forestgreen", `adm-pos-convert` = "blue",
    `secondary-convert` = "gray", `ambiguous-adm-pos` = "turquoise3", `ambiguous-convert`
    = "deeppink3"),
  include_trace = TRUE,
  include_surv = TRUE,
  include_patient = TRUE,
  title_size = 10,
  text_size = 8,
  key_size = 0.5,
  layout = c("horizontal", "vertical")
)

Arguments

trace_colors: Color palette for trace location values; should match plot_trace_phylo_tree().
trace_labels: Character vector of labels per trace location; length should match trace_colors.
surv_colors: Named colors for surveillance types; should match plot_trace_phylo_tree().
surv_shapes: Named integer plotting shapes for surveillance types; should match plot_trace_phylo_tree().
label_colors: Named colors for patient category labels; should match plot_trace_phylo_tree().
include_trace: Logical. Include the trace location legend.
include_surv: Logical. Include the surveillance legend.
include_patient: Logical. Include the patient category legend.
title_size: Numeric. Font size for legend titles.
text_size: Numeric. Font size for legend text.
key_size: Numeric. Size of legend keys in cm.
layout: Character. "horizontal" places legends side-by-side, "vertical" stacks them.

Value

A ggplot object containing only the legend(s), suitable for saving with ggsave().