plot_compare_indels: Compare two indel mutation profiles

In CuppenResearch/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Compare two indel mutation profiles

Description

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

Usage

plot_compare_indels(
  profile1,
  profile2,
  profile_names = c("profile 1", "profile 2"),
  profile_ymax = 0.2,
  diff_ylim = c(-0.1, 0.1)
)

Arguments

profile1	First mutation profile
profile2	Second 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(-0.1, 0.1)

Value

A ggplot2 object

See Also

plot_compare_profiles, plot_compare_dbs, plot_compare_mbs

Other Indels: count_indel_contexts(), get_indel_context(), plot_indel_contexts(), plot_main_indel_contexts()

Examples

## Get the indel counts
## See 'count_indel_contexts()' for more info on how to do this.
indel_counts <- readRDS(system.file("states/blood_indel_counts.rds",
  package = "MutationalPatterns"
))

## Get indel refit info.
## See 'fit_to_signatures()' for more info on how to do this.
fit_res <- readRDS(system.file("states/indel_refit.rds",
  package = "MutationalPatterns"
))

## Compare the reconstructed profile of sample 1 with the original profile
## The same thing could be done with a reconstructed profile from NMF.
plot_compare_indels(indel_counts[, 1], fit_res$reconstructed[, 1])

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

## Or change the names of the profiles
plot_compare_indels(indel_counts[, 1],
  indel_counts[, 2],
  profile_names = c("Original", "Reconstructed")
)

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

CuppenResearch/MutationalPatterns documentation built on Nov. 23, 2022, 4:13 a.m.