plotPeriodicityResults {periodicDNA} | R Documentation

## Plot the output of getPeriodicity()

### Description

This function plots some results from the result of getPeriodicity(). It plots the raw distogram, the distance-decay normalized distogram and the resulting PSD values. If a shuffled control has been performed by getPeriodicity(), it also displays it.

### Usage

    plotPeriodicityResults(
      results,
      periods = c(2, 20),
      filter_periods = TRUE,
      facet_control = TRUE,
      xlim = NULL,
      fdr_threshold = 0.05,
      ...
    )

### Arguments

`results` | The output of getPeriodicity function.
`periods` | Vector a numerical vector of length 2, to specify the x-axis limits
`filter_periods` | Boolean Should the x-axis be constrained to the periods?
`facet_control` | Boolean should the shuffling plots be faceted?
`xlim` | Integer x axis upper limit in raw and norm. distograms
`fdr_threshold` | Float, significance threshold
`...` | Additional theme arguments passed to theme_ggplot2()

### Value

list A list containing four ggplots

### Examples

    data(ce11_TSSs)
    periodicity_result <- getPeriodicity(
        ce11_TSSs[['Ubiq.']][1:100],
        genome = 'BSgenome.Celegans.UCSC.ce11',
        motif = 'TT',
        BPPARAM = setUpBPPARAM(1)
    )
    head(periodicity_result$PSD)
    plotPeriodicityResults(periodicity_result)
    plotPeriodicityResults(periodicity_result, xlim = 150)
    plotPeriodicityResults(
        periodicity_result, xlim = 150, filter_periods = FALSE
    )
    plotPeriodicityResults(
        periodicity_result, xlim = 150, facet_control = FALSE
    )

[Package periodicDNA version 1.4.0 Index]