Plot a phylogeny with a presence/absence trace heatmap and surveillance overlay — plot_trace_phylo

Creates a combined visualization of a phylogenetic tree with a patient presence/absence trace heatmap. Surveillance data is encoded directly into cell colors (not dots): dark gray for presence, white for absence, and surveillance colors for results.

Usage

plot_trace_phylo_presence(
  tree,
  isolate_lookup,
  trace_data,
  surv_df,
  cluster_filter = NULL,
  presence_color = "gray85",
  surv_colors = c(neg = "blue", pos = "red")
)

Arguments

tree: A phylogenetic tree of class phylo.
isolate_lookup: Data frame from get_isolate_lookup() with columns isolate_id, patient_id, date, cluster, adm_pos, prev_surv.
trace_data: Binary matrix (0/1) with patient IDs as row names and dates as column names.
surv_df: Surveillance data frame with columns patient_id, genome_id, surv_date, result (0/1 for negative/positive).
cluster_filter: Cluster IDs to include, or NULL for all.
presence_color: Color for presence cells.
surv_colors: Named colors for the negative and positive surveillance types.

Value

A ggplot object combining the tree, heatmap, and surveillance overlay.