Plot joint prior distribution of total copy number and multiplicity

Visualises the joint prior distribution of total copy number (\(k\)) and mutation multiplicity (\(m\)) for each mutation in a sample. The most likely configuration for each mutation is highlighted.

Usage

plot_prior_k_m(priors_k_m, x, k_max)

Arguments

priors_k_m

Prior distribution object for joint \(k,m\).

x

An INCOMMON object.

k_max

Integer specifying the maximum total copy number.

Value

A faceted ggplot2 contour plot showing the joint prior distribution of copy number and multiplicity for each mutation.

Examples

if (FALSE) { # \dontrun{
# plot_prior_k_m requires a classified INCOMMON object (see ?classify)
data(MSK_genomic_data)
data(MSK_clinical_data)
data(priors_pcawg_hmf)
data(priors_eta)
sample = 'P-0002081'
x = init(
  genomic_data = MSK_genomic_data[MSK_genomic_data$sample == sample,],
  clinical_data = MSK_clinical_data[MSK_clinical_data$sample == sample,]
)
x = classify(
  x = x, priors_k_m = priors_pcawg_hmf, priors_eta = priors_eta,
  num_cores = 1, iter_warmup = 10, iter_sampling = 10, num_chains = 1
)
plot_prior_k_m(priors_k_m = x$priors_k_m, x = x, k_max = 8)
} # }