Plot genome-wide coverage.

Plot a genome-wide scatter plot of mutation depths. The function can randomly subset the points to show.

plot_gw_depth(x, N = 5000, chromosomes = paste0("chr", c(1:22, "X", "Y")))

Arguments

x

A CNAqc object.

N

Mutations to use, randomly sampled.

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.

plot_gw_depth(x)
#> Warning: Removed 24 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 24 rows containing missing values or values outside the scale range
#> (`geom_rect()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_hline()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_hline()`).


# Downsampling examples
plot_gw_depth(x, N = 100)
#> Warning: Removed 24 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 24 rows containing missing values or values outside the scale range
#> (`geom_rect()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_hline()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_hline()`).

plot_gw_depth(x, N = 1000)
#> Warning: Removed 24 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 24 rows containing missing values or values outside the scale range
#> (`geom_rect()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_hline()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_hline()`).

plot_gw_depth(x, N = 10000)
#> Warning: Removed 24 rows containing missing values or values outside the scale range
#> (`geom_segment()`).
#> Warning: Removed 24 rows containing missing values or values outside the scale range
#> (`geom_rect()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_hline()`).
#> Warning: Removed 1 row containing missing values or values outside the scale range
#> (`geom_hline()`).