Plot signal along genome before and after TangentXY normalization

Usage

plot_signal_along_loci(
  tnorm,
  sample_id,
  pif_df,
  tsig_df,
  n_latent,
  output_dir = NULL
)

Arguments

tnorm: A normalized tumor signal matrix output by run_tangent, or a list of such matrices.
sample_id: Sample ID to plot
pif_df: Tibble or filepath to a text file containing probe information. Should have a 'chr' column with chromosome names (1-22, X, Y) and an 'arm' column with arm names (p or q)
tsig_df: Tibble or filepath to a text file containing the tumor signal matrix
n_latent: A numeric vector of the numbers of latent factors used in TangentXY normalization. Should correspond to the elements in tnorm.
output_dir: Directory to save the plot. If NULL, the plot will be printed to the screen.

Value

(Invisibly) A ggplot object containing the signal profiles for the sample before and after normalization.

Examples

n_latent <- c(5, 10)
tangent_res <- lapply(n_latent, function(nlf) {
  run_tangent(example_sif, example_nsig_df, example_tsig_df, nlf, make_plots = FALSE)
})
#> 
#> Applying linear transformation ...
#> 
#> Running SVD ...
#> 
#> Running Tangent on autosomes and chrX ...
#> Done.
#> 
#> Running Tangent on male chrY ...
#> Done.
#> 
#> Applying linear transformation ...
#> 
#> Running SVD ...
#> 
#> Running Tangent on autosomes and chrX ...
#> Done.
#> 
#> Running Tangent on male chrY ...
#> Done.
plot_signal_along_loci(tangent_res, "tumor.female2", example_pif,
                       example_tsig_df, n_latent = n_latent)