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