plot_phylo_heatmap: Plot single-cell CNV calls along with the clonal phylogeny

Description

Plot single-cell CNV calls along with the clonal phylogeny

Usage

plot_phylo_heatmap(
  gtree,
  joint_post,
  segs_consensus,
  clone_post = NULL,
  p_min = 0.9,
  annot = NULL,
  pal_annot = NULL,
  annot_title = "Annotation",
  annot_scale = NULL,
  clone_dict = NULL,
  clone_bar = TRUE,
  clone_stack = TRUE,
  pal_clone = NULL,
  clone_title = "Genotype",
  clone_legend = TRUE,
  line_width = 0.1,
  tree_height = 1,
  branch_width = 0.2,
  tip_length = 0.2,
  annot_bar_width = 0.25,
  clone_bar_width = 0.25,
  bar_label_size = 7,
  tvn_line = TRUE,
  clone_line = FALSE,
  exclude_gap = FALSE,
  root_edge = TRUE,
  raster = FALSE,
  show_phylo = TRUE
)

Value

ggplot panel

Arguments

gtree: tbl_graph The single-cell phylogeny
joint_post: dataframe Joint single cell CNV posteriors
segs_consensus: datatframe Consensus segment dataframe
clone_post: dataframe Clone assignment posteriors
p_min: numeric Probability threshold to display CNV calls
annot: dataframe Cell annotations, dataframe with 'cell' and additional annotation columns
pal_annot: named vector Colors for cell annotations
annot_title: character Legend title for the annotation bar
annot_scale: ggplot scale Color scale for the annotation bar
clone_dict: named vector Clone annotations, mapping from cell name to clones
clone_bar: logical Whether to display clone bar plot
clone_stack: character Whether to plot clone assignment probabilities as stacked bar
pal_clone: named vector Clone colors
clone_title: character Legend title for the clone bar
clone_legend: logical Whether to display the clone legend
line_width: numeric Line width for CNV heatmap
tree_height: numeric Relative height of the phylogeny plot
branch_width: numeric Line width in the phylogeny
tip_length: numeric Length of tips in the phylogeny
annot_bar_width: numeric Width of annotation bar
clone_bar_width: numeric Width of clone genotype bar
bar_label_size: numeric Size of sidebar text labels
tvn_line: logical Whether to draw line separating tumor and normal cells
clone_line: logical Whether to display borders for clones in the heatmap
exclude_gap: logical Whether to mark gap regions
root_edge: logical Whether to plot root edge
raster: logical Whether to raster images
show_phylo: logical Whether to display phylogeny on y axis

Examples

Run this code

p = plot_phylo_heatmap(
    gtree = phylogeny_example,
    joint_post = joint_post_example,
    segs_consensus = segs_example)

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