Plot a phylogenetic tree with VAF heatmap and annotations

Usage

plot_phylo_heatmap2(
  phylo,
  df_var = NULL,
  branch_width = 0.25,
  root_edge = TRUE,
  dot_size = 1,
  ylim = NULL,
  min_cells = 1,
  tip_annot = NULL,
  annot_scale = NULL,
  feature_mat = NULL,
  feature_limits = c(-2, 2),
  feature_scale = NULL,
  rescale = FALSE,
  title = NULL,
  ytitle = NULL,
  xtitle = NULL,
  label_site = FALSE,
  cell_annot = NULL,
  tip_lab = FALSE,
  node_lab = FALSE,
  layered = FALSE,
  annot_bar_height = 0.1,
  clade_bar_height = 1,
  feature_height = 1,
  het_max = 0.1,
  conf_min = 0,
  conf_max = 1,
  conf_label = FALSE,
  branch_length = TRUE,
  node_conf = FALSE,
  annot_pal = NULL,
  annot_legend = FALSE,
  label_group = FALSE,
  text_size = 3,
  annot_title_size = text_size,
  node_label_size = 1,
  mut = NULL,
  mark_low_cov = FALSE,
  facet_by_group = FALSE,
  flip = TRUE,
  ladderize = TRUE,
  node_scores = NULL,
  node_score_limits = c(-4, 4),
  variants_highlight = NULL,
  show_variant_names = TRUE,
  show_tree_y_axis = FALSE,
  feature_legend = TRUE,
  raster = FALSE,
  raster_dpi = 300
)

Arguments

df_var: Optional data frame of variant calls with columns cell, variant, and either vaf or a/d for computing VAF.
branch_width: Numeric branch line width for the tree.
root_edge: Logical; included for compatibility with earlier calls.
dot_size: Numeric size for tip/node points.
ylim: Optional y-axis limits (unused in current implementation).
min_cells: Integer minimum number of cells with VAF > 0 required to keep a variant.
tip_annot: Optional data frame of tip annotations with columns cell and annot.
annot_scale: Optional ggplot scale for annotation colors.
feature_mat: Optional matrix of features (rows = features, columns = cells) to plot as a heatmap.
feature_limits: Numeric vector of length 2 giving limits for feature heatmap color scale.
feature_scale: Optional ggplot scale for feature heatmap colors.
rescale: Logical; if TRUE, z-score features per row before plotting.
title: Optional plot title.
ytitle: Optional VAF heatmap y-axis title.
xtitle: Optional VAF heatmap x-axis title.
label_site: Logical; included for compatibility with earlier calls.
cell_annot: Optional data frame or list of data frames for annotation bars.
tip_lab: Logical; if TRUE, show tip labels on the tree.
node_lab: Logical; if TRUE, show internal node labels on the tree.
layered: Logical; if TRUE, render annotation bars as layered tiles.
annot_bar_height: Numeric height for each annotation bar panel.
clade_bar_height: Numeric height for clade bar panel (unused in current implementation).
feature_height: Numeric height for the feature heatmap panel.
het_max: Numeric maximum VAF for heatmap color scaling.
conf_min: Numeric minimum value for confidence color scale.
conf_max: Numeric maximum value for confidence color scale.
conf_label: Logical; if TRUE, label node confidence values.
branch_length: Logical; if FALSE, drop branch lengths before plotting.
node_conf: Logical; if TRUE, plot node confidence (requires tbl_graph).
annot_pal: Optional palette (vector or list) for annotation bars.
annot_legend: Logical; if TRUE, show annotation legends.
label_group: Logical; if TRUE, label groups in annotation bars.
text_size: Numeric base text size for labels.
annot_title_size: Numeric size for annotation strip titles.
node_label_size: Numeric size for node/tip labels.
mut: Optional mutation column name in tree to color nodes by VAF.
mark_low_cov: Logical; if TRUE, mark low-coverage cells on the VAF heatmap.
facet_by_group: Logical; if TRUE, facet VAF heatmap by group column.
flip: Logical; if TRUE, flip the tree orientation.
ladderize: Logical; if TRUE, ladderize the tree.
node_scores: Optional named numeric vector of node/tip scores used to color tree branches. Names may be tip labels, internal node labels, or numeric node IDs.
node_score_limits: Numeric vector of length 2 giving limits for node score colors.
variants_highlight: Optional vector of variant names to bold on the heatmap axis.
show_variant_names: Logical; if TRUE, show variant tick labels on the VAF heatmap; hide when FALSE.
show_tree_y_axis: Logical; if TRUE, show y-axis ticks/labels on the tree panel.
feature_legend: Logical; if TRUE, display the legend for the feature heatmap; otherwise hide it.
raster: Logical; if TRUE, rasterize each plot panel via ggrastr.
raster_dpi: Numeric DPI to use when rasterizing panels.
tree: A phylo object or tbl_graph tree.

Value

A patchwork/ggplot object combining the tree, annotations, and heatmaps.