plot_phylo_heatmap {numbat}

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
)

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

Value

ggplot panel

Examples

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