Plot Circular Phylogenetic Tree with Annotations — plot_phylo

Creates a circular (fan) layout phylogenetic tree plot with optional annotations, feature heatmaps, and node confidence values.

Usage

plot_phylo_circ(
  gtree,
  cell_annot = NULL,
  tip_annot = NULL,
  feature_mat = NULL,
  branch_scores = NULL,
  node_conf = FALSE,
  conf_label = FALSE,
  title = "",
  pwidth_annot = 0.25,
  pwidth_feature = 0.25,
  branch_width = 0.3,
  dot_size = 1,
  conf_min = 0,
  conf_max = 0.5,
  annot_pal = NULL,
  offset = 0.05,
  width = 0.8,
  label_size = 2,
  rescale = FALSE,
  limits = c(-2, 2),
  feature_legend_title = "Score",
  flip = TRUE,
  annot_legend = TRUE,
  feature_legend = TRUE,
  layered = FALSE,
  smooth_k = 0,
  ladderize = TRUE,
  open_angle = 0,
  feature_axis_label = TRUE,
  feature_axis_angle = 30
)

Arguments

gtree: A phylo object or tbl_graph object representing the tree.
cell_annot: A data frame or list of data frames containing cell annotations. Columns should include 'cell' and 'annot'.
tip_annot: A data frame containing tip annotations. Columns should include 'cell' and 'annot'.
feature_mat: A matrix of features to plot as a heatmap (rows are features, columns are cells).
branch_scores: Optional branch scores (currently unused).
node_conf: Logical. If TRUE and gtree is a tbl_graph, plots node confidence.
conf_label: Logical. If TRUE, adds text labels for node confidence.
title: Character string for the plot title.
pwidth_annot: Numeric. Width of the annotation ring(s).
pwidth_feature: Numeric. Width of the feature heatmap ring.
branch_width: Numeric. Line width for tree branches.
dot_size: Numeric. Size of tip/node points.
conf_min: Numeric. Minimum value for confidence color scale.
conf_max: Numeric. Maximum value for confidence color scale.
annot_pal: A vector or list of vectors specifying colors for annotations.
offset: Numeric. Offset distance between tree and annotation rings.
width: Numeric. Width of heatmap cells.
label_size: Numeric. Size of text labels.
rescale: Logical. If TRUE, rescales features (z-score) for the heatmap.
limits: Numeric vector of length 2. Limits for the feature heatmap color scale.
feature_legend_title: Character string. Title for the feature heatmap legend.
flip: Logical. If TRUE, flips the tree direction.
layered: Logical. If TRUE, plots annotations as layered tiles.
smooth_k: Integer. Number of neighbors for smoothing features. 0 means no smoothing.
ladderize: Logical. If TRUE, ladderizes the tree.
open_angle: Numeric. Angle of the opening in the fan layout.
feature_axis_label: Logical. If TRUE, show feature heatmap axis labels; hide when FALSE.
feature_axis_angle: Numeric. Rotation angle (degrees) for feature axis text.
legend: Logical. If TRUE, shows legends.

Value

A ggtree plot object.