plot_compare_profiles {MutationalPatterns} | R Documentation

## Compare two 96 mutation profiles

### Description

Plots two 96 mutation profiles and their difference, reports the residual sum of squares (RSS).

### Usage

    plot_compare_profiles(
      profile1,
      profile2,
      profile_names = c("profile 1", "profile 2"),
      profile_ymax = 0.2,
      diff_ylim = c(-0.02, 0.02),
      colors = NA,
      condensed = FALSE
    )

### Arguments

`profile1` | First 96 mutation profile
`profile2` | Second 96 mutation profile
`profile_names` | Character vector with names of the mutations profiles used for plotting, default = c("profile 1", "profile 2")
`profile_ymax` | Maximum value of y-axis (relative contribution) for profile plotting. This can only be used to increase the y axis. If bars fall outside this limit, the maximum value is automatically increased. default = 0.2.
`diff_ylim` | Y-axis limits for profile difference plot, default = c(-0.02, 0.02)
`colors` | 6 value color vector
`condensed` | More condensed plotting format. Default = F.

### Value

96 spectrum plot of profile 1, profile 2 and their difference

### See Also

`mut_matrix`, `extract_signatures`, `plot_compare_indels`, `plot_compare_dbs`, `plot_compare_mbs`

### Examples

    ## See the 'mut_matrix()' example for how we obtained the following
    ## 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"
    ))

    ## Compare the reconstructed 96-profile of sample 1 with the original profile
    ## The same thing could be done with a reconstructed profile from signature refitting.
    plot_compare_profiles(mut_mat[, 1],
      nmf_res$reconstructed[, 1],
      profile_names = c("Original", "Reconstructed")
    )

    ## You could also compare regular mutation profiles with eachother.
    plot_compare_profiles(
      mut_mat[, 1],
      mut_mat[, 2]
    )

    ## You can also change the y limits.
    ## This can be done separately for the profiles and the different facets.
    plot_compare_profiles(mut_mat[, 1],
      mut_mat[, 2],
      profile_ymax = 0.3,
      diff_ylim = c(-0.03, 0.03)
    )

[Package MutationalPatterns version 3.0.1 Index]