Draw a composite phylogenetic tree + cell-by-variant heatmap for mtDNA data.
Usage
plot_tree_heatmap_teng_cw(
gtree,
df_var,
draw_depth,
branch_width = 0.25,
root_edge = TRUE,
dot_size = 1,
ylim = NULL,
clade_annot = NULL,
tip_annot = NULL,
title = NULL,
label_site = FALSE,
cell_annot = NULL,
tip_lab = FALSE,
node_lab = FALSE,
layered = FALSE,
annot_bar_height = 0.1,
clade_bar_height = 1,
het_max = 0.1,
conf_min = 0.5,
conf_max = 0.5,
conf_label = FALSE,
branch_length = TRUE,
node_conf = FALSE,
annot_scale = NULL,
annot_legend = FALSE,
label_group = FALSE,
annot_legend_title = "",
text_size = 3,
label_size = 1,
mut = NULL,
post_max = FALSE,
mark_low_cov = FALSE,
facet_by_group = FALSE,
flip = FALSE
)Arguments
- gtree
A phylo or tbl_graph object representing the clonal tree.
- df_var
A data.frame with at least columns: cell, variant, a (alt), d (depth), or a precomputed vaf column between 0 and 1.
- draw_depth
Logical; draw branch width by depth when available.
- branch_width
Numeric scaling for branch width drawing.
- root_edge
Logical; whether to include a root edge.
- dot_size
Numeric size for node/tip dots.
- ylim
Optional y limits.
- clade_annot
Optional data.frame of clade annotations with columns cell, clade, and optional score.
- tip_annot
Optional data.frame of tip annotations (columns: cell, annot).
- title
Optional plot title.
- label_site
Logical; label mutational sites on the tree.
- cell_annot
Either a single data.frame (columns: cell, annot) or a named list of such data.frames; each element produces a stacked annotation bar.
- tip_lab, node_lab
Logical; show tip/node labels.
- layered
Logical; layered rendering for annotation bars.
- annot_bar_height, clade_bar_height
Numeric heights for stacked bars.
- het_max
Numeric VAF max for color scale.
- conf_min, conf_max
Numeric limits for node confidence fill.
- conf_label
Logical; render numeric confidence labels.
- branch_length
Logical; use branch lengths if available.
- node_conf
Logical; display internal node confidence.
- annot_scale
Optional scaling for annotation bars.
- annot_legend, label_group
Logical flags controlling annotation display.
- annot_legend_title
Character legend title used when cell_annot is a single table (named list elements use their own names as titles).
- text_size, label_size
Numeric text sizes.
- mut
Optional column name in node data to color nodes by.
- post_max, mark_low_cov, facet_by_group, flip
Additional display flags.