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

In whtns/numbat: Haplotype-Aware CNV Analysis from scRNA-Seq

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,
  annot = NULL,
  pal_annot = NULL,
  annot_title = "Annotation",
  annot_scale = NULL,
  clone_dict = NULL,
  clone_bar = FALSE,
  pal_clone = NULL,
  clone_title = "Genotype",
  clone_legend = TRUE,
  p_min = 0.9,
  line_width = 0.1,
  tree_height = 1,
  branch_width = 0.2,
  tip_length = 0.2,
  clone_line = FALSE,
  superclone = FALSE,
  exclude_gap = FALSE,
  root_edge = TRUE,
  raster = FALSE
)

Arguments

gtree	tbl_graph The single-cell phylogeny
joint_post	dataframe Joint single cell CNV posteriors
segs_consensus	datatframe Consensus segment dataframe
annot	named vector Cell annotations, keys are cell names
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
pal_clone	named vector Clone colors
clone_title	character Legend title for the clone bar
clone_legend	logical Whether to display the clone legend
p_min	numeric Probability threshold to display CNV calls
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
clone_line	logical Whether to display borders for clones in the heatmap
superclone	logical Wehether to display superclones in the clone bar
exclude_gap	logical Whether to mark gap regions
root_edge	logical Whether to plot root edge
raster	logical Whether to raster images

Value

ggplot panel

Examples

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

whtns/numbat documentation built on Nov. 8, 2022, 10:48 a.m.