plot_spectrum {MutationalPatterns} | R Documentation

## Plot point mutation spectrum

### Description

Plot point mutation spectrum

### Usage

    plot_spectrum(
      type_occurrences,
      CT = FALSE,
      by = NA,
      indv_points = FALSE,
      error_bars = c("95%_CI", "stdev", "SEM", "none"),
      colors = NA,
      legend = TRUE,
      condensed = FALSE
    )

### Arguments

`type_occurrences` | Type occurrences matrix
`CT` | Distinction between C>T at CpG and C>T at other sites, default = FALSE
`by` | Optional grouping variable
`indv_points` | Whether to plot the individual samples as points, default = FALSE
`error_bars` | The type of error bars to plot. * '95 * 'stdev' for standard deviations; * 'SEM' for the standard error of the mean (NOT recommended); * 'none' Do not plot any error bars;
`colors` | Optional color vector with 7 values
`legend` | Plot legend, default = TRUE
`condensed` | More condensed plotting format. Default = F.

### Value

Spectrum plot

### See Also

`read_vcfs_as_granges`, `mut_type_occurrences`

### Examples

    ## See the 'read_vcfs_as_granges()' example for how we obtained the
    ## following data:
    vcfs <- readRDS(system.file("states/read_vcfs_as_granges_output.rds",
      package = "MutationalPatterns"
    ))

    ## Load a reference genome.
    ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
    library(ref_genome, character.only = TRUE)

    ## Get the type occurrences for all VCF objects.
    type_occurrences <- mut_type_occurrences(vcfs, ref_genome)

    ## Plot the point mutation spectrum over all samples
    plot_spectrum(type_occurrences)

    ## Or with distinction of C>T at CpG sites
    plot_spectrum(type_occurrences, CT = TRUE)

    ## You can also include individual sample points.
    plot_spectrum(type_occurrences, CT = TRUE, indv_points = TRUE)

    ## You can also change the type of error bars
    plot_spectrum(type_occurrences, error_bars = "stdev")

    ## Or plot spectrum per tissue
    tissue <- c(
      "colon", "colon", "colon",
      "intestine", "intestine", "intestine",
      "liver", "liver", "liver"
    )

    plot_spectrum(type_occurrences, by = tissue, CT = TRUE)

    ## Or plot the spectrum per sample. Error bars are set to 'none', because they can't be plotted.
    plot_spectrum(type_occurrences, by = names(vcfs), CT = TRUE, error_bars = "none")

    ## Plot it in a more condensed manner,
    ## which is is ideal for publications.
    plot_spectrum(type_occurrences,
    by = names(vcfs),
    CT = TRUE,
    error_bars = "none",
    condensed = TRUE)

    ## You can also set custom colors.
    my_colors <- c(
      "pink", "orange", "blue", "lightblue",
      "green", "red", "purple"
    )

    ## And use them in a plot.
    plot_spectrum(type_occurrences,
      CT = TRUE,
      legend = TRUE,
      colors = my_colors
    )

[Package MutationalPatterns version 3.0.1 Index]