plot_enrichment_depletion {MutationalPatterns} | R Documentation

## Plot enrichment/depletion of mutations in genomic regions

### Description

Plot enrichment/depletion of mutations in genomic regions

### Usage

    plot_enrichment_depletion(df, sig_type = c("fdr", "p"))

### Arguments

`df` | Dataframe result from enrichment_depletion_test()
`sig_type` | The type of significance to be used. Possible values: * 'fdr' False discovery rate. A type of multiple testing correction.; * 'p' for regular p values.

### Value

Plot with two parts. 1: Barplot with no. mutations expected and observed per region. 2: Effect size of enrichment/depletion (log2ratio) with results significance test.

### See Also

`enrichment_depletion_test`, `genomic_distribution`

### Examples

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

    tissue <- c(
      "colon", "colon", "colon",
      "intestine", "intestine", "intestine",
      "liver", "liver", "liver"
    )

    ## Perform the enrichment/depletion test.
    distr_test <- enrichment_depletion_test(distr, by = tissue)

    ## Plot the enrichment/depletion
    plot_enrichment_depletion(distr_test)

    #Perform and plot the enrichmet depletion test for all samples pooled
    distr_test2 <- enrichment_depletion_test(distr)
    plot_enrichment_depletion(distr_test2)

    ## Plot with p values instead of fdr
    plot_enrichment_depletion(distr_test, sig_type = "p")

    ## Use multiple (max 3) significance cutoffs.
    ## This will vary the number of significance stars.
    distr_multistars <- enrichment_depletion_test(distr,
      by = tissue,
      p_cutoffs = c(0.05, 0.01, 0.005),
      fdr_cutoffs = c(0.1, 0.05, 0.01)
    )
    plot_enrichment_depletion(distr_multistars)

[Package MutationalPatterns version 3.0.1 Index]