Plot a ctree tree. — plot.ctree • ctree

This S3 method plots a ctree tree, using ggraph layout functions. The tree is annotated and coloured in each node (i.e., cluster) that contain a driver event annotated. The driver id is also reported via ggrepel annotation functions.

Usage

# S3 method for ctree
plot(
  x,
  node_palette = colorRampPalette(RColorBrewer::brewer.pal(n = 9, "Set1")),
  tree_layout = "tree",
  ...
)

Arguments

x: A ctree tree.
node_palette: A function that applied to a number will return a set of colors. By default this is a colorRampPalette applied to 9 colours of the RColorBrewer palette Set1. Colors are generated following a topological sort of the information transfer, which is obtained from igraph.
tree_layout: A layout that can be used by tidygraph, which wraps igraph's layouts. By default this is a `tree` layout.
...: Extra S3 parameters

Value

A ggplot plot of the tree.

Examples

data('ctree_input')

x = ctrees(
   ctree_input$CCF_clusters,
   ctree_input$drivers,
   ctree_input$samples,
   ctree_input$patient,
   ctree_input$sspace.cutoff,
   ctree_input$n.sampling,
   ctree_input$store.max
   )
#>  [ ctree ~ clone trees generator for CUK12345 ] 
#> 
#> # A tibble: 7 × 7
#>   cluster nMuts is.driver is.clonal    R1    R2    R3
#>   <chr>   <int> <lgl>     <lgl>     <dbl> <dbl> <dbl>
#> 1 1          72 TRUE      FALSE      0     0.92  0   
#> 2 2          69 TRUE      TRUE       0.99  0.98  0.99
#> 3 3          48 FALSE     FALSE      0     0     0.49
#> 4 4          29 FALSE     FALSE      0.01  0.01  0.93
#> 5 5          24 TRUE      FALSE      0.78  0     0   
#> 6 6          23 TRUE      FALSE      0.98  0.03  0.98
#> 7 7          15 FALSE     FALSE      0     0.41  0   
#> 
#> ✔ Trees per region 1, 3, 1
#> ℹ Total 3 tree structures - search is exahustive
#> 
#> ── Ranking trees 
#> ✔ 3  trees with non-zero score, storing 3
   
plot(x[[1]])
#> Warning: Duplicated aesthetics after name standardisation: na.rm
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Warning: Removed 1 rows containing missing values (geom_point).