Visualise the prior distribution over the rate of reads per chromosome copy.

Visualise the prior distribution over the rate of reads per chromosome copy.

Usage

plot_eta_prior(x, priors_eta)

Arguments

x

An object of class INCOMMON.'

priors_eta

A table with the prior distribution on the rate of reads per chromosome copy as obtained with function compute_eta_prior.

Examples

# Load the default prior on eta, estimated from the MKS-MET data and the data.
data(MSK_genomic_data)
data(MSK_clinical_data)
data(priors_eta)
x = init(genomic_data = MSK_genomic_data, clinical_data =MSK_clinical_data)
#> ── INCOMMON - Inference of copy number and mutation multiplicity in oncology ───
#> 
#> ── Genomic data ──
#> 
#> ✔ Found 25659 samples, with 224939 mutations in 491 genes
#> ! No read counts found for 1393 mutations in 1393 samples
#> ! Gene name not provided for 1393 mutations
#> ! 201 genes could not be assigned a role (TSG or oncogene)
#> 
#> ── Clinical data ──
#> 
#> ℹ Provided clinical features:
#> 
#> ✔ sample (required for classification)
#> ✔ purity (required for classification)
#> ✔ tumor_type
#> ✔ OS_MONTHS
#> ✔ OS_STATUS
#> ✔ SAMPLE_TYPE
#> ✔ MET_COUNT
#> ✔ METASTATIC_SITE
#> ✔ MET_SITE_COUNT
#> ✔ PRIMARY_SITE
#> ✔ SUBTYPE_ABBREVIATION
#> ✔ GENE_PANEL
#> ✔ SEX
#> ✔ TMB_NONSYNONYMOUS
#> ✔ FGA
#> ✔ AGE_AT_SEQUENCING
#> ✔ RACE
#> 
#> ✔ Found 25257 matching samples
#> ✖ Found 513 unmatched samples
# Plot classification results for a specific sample
plot_eta_prior(x = x, priors_eta = priors_eta)
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Warning: Unknown or uninitialised column: `cohort`.
#> Picking joint bandwidth of 36.2
#> Warning: Removed 1681 rows containing non-finite outside the scale range
#> (`stat_density_ridges()`).