Plot the output of getPeriodicity()

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.

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)
)
#> - Mapping k-mers.
#> - 97937 pairwise distances measured.
#> - Calculating pairwise distance distribution.
#> - Normalizing distogram vector.
#> - Applying Fast Fourier Transform to the normalized distogram.
head(periodicity_result$PSD)
#>    freq    period          PSD
#> 1 0.005 200.00000 5.283741e-08
#> 2 0.010 100.00000 3.937510e-08
#> 3 0.015  66.66667 4.057825e-08
#> 4 0.020  50.00000 1.233001e-08
#> 5 0.025  40.00000 2.084665e-08
#> 6 0.030  33.33333 7.776985e-08
plotPeriodicityResults(periodicity_result)
plotPeriodicityResults(periodicity_result, xlim = 150)
plotPeriodicityResults(
    periodicity_result, xlim = 150, filter_periods = FALSE
)
plotPeriodicityResults(
    periodicity_result, xlim = 150, facet_control = FALSE
)