plot_original_vs_reconstructed {MutationalPatterns} | R Documentation

## Plot the similarity between a mutation matrix and its reconstructed profile

### Description

When a reconstructed profile has a cosine similarity of more than 0.95 with original, the reconstructed profile is considered very good.

### Usage

    plot_original_vs_reconstructed(
      mut_matrix,
      reconstructed,
      y_intercept = 0.95,
      ylims = c(0.6, 1)
    )

### Arguments

`mut_matrix` | mutation count matrix (dimensions: x mutation types X n samples)
`reconstructed` | A reconstructed mutation count matrix
`y_intercept` | The y intercept of the plotted horizontal line. Default: 0.95.
`ylims` | The limits of the y axis. Default: c(0.6, 1)

### Value

A ggplot figure

### Examples

    ## See the 'mut_matrix()' example for how we obtained the mutation matrix:
    mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
      package = "MutationalPatterns"
    ))

    ## Extracting signatures can be computationally intensive, so
    ## we use pre-computed data generated with the following command:
    # nmf_res <- extract_signatures(mut_mat, rank = 2)

    nmf_res <- readRDS(system.file("states/nmf_res_data.rds",
      package = "MutationalPatterns"
    ))

    ## Create figure
    plot_original_vs_reconstructed(mut_mat, nmf_res$reconstructed)

    ## You can also use the results of signature refitting.
    ## Here we load some data as an example
    fit_res <- readRDS(system.file("states/snv_refit.rds",
      package = "MutationalPatterns"
    ))
    plot_original_vs_reconstructed(mut_mat, fit_res$reconstructed)

    ## You can also change the height of the horizontal line
    plot_original_vs_reconstructed(mut_mat, fit_res$reconstructed, y_intercept = 0.90)

    ## It's also possible to change the limits of the y axis
    plot_original_vs_reconstructed(mut_mat, fit_res$reconstructed, ylims = c(0, 1))

[Package MutationalPatterns version 3.0.1 Index]