Plot counts and numbers of clonal simple CNAs.

Plot a barplot for the segments, reporting either their counts of the proportion of genome covered.

plot_karyotypes(
  x,
  type = "percentage",
  chromosomes = paste0("chr", c(1:22, "X", "Y"))
)

Arguments

x

A CNAqc object.

type

With "percentage", the proportion of genome covered is returned. With "number", the segment counts. In all other cases an erorr is generated.

chromosomes

The chromosome to use for this plot.

Value

A ggplot2 plot.

Examples

data('example_dataset_CNAqc', package = 'CNAqc')
x = init(mutations = example_dataset_CNAqc$mutations, cna = example_dataset_CNAqc$cna, purity = example_dataset_CNAqc$purity)
#> 
#> ── CNAqc - CNA Quality Check ───────────────────────────────────────────────────
#> 
#> ℹ Using reference genome coordinates for: GRCh38.
#> ✔ Found annotated driver mutations: TTN, CTCF, and TP53.
#> ✔ Fortified calls for 12963 somatic mutations: 12963 SNVs (100%) and 0 indels.
#> ! CNAs have no CCF, assuming clonal CNAs (CCF = 1).
#> ✔ Fortified CNAs for 267 segments: 267 clonal and 0 subclonal.
#> ✔ 12963 mutations mapped to clonal CNAs.

# All chromosomes (default)
plot_karyotypes(x)


# Specific chromosomes
plot_karyotypes(x, chromosomes = 'chr3')
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.
#> Warning: No shared levels found between `names(values)` of the manual scale and the
#> data's fill values.

plot_karyotypes(x, chromosomes = 'chr13')