plotPhasogram: Plot annotated phasogram.

In fmicompbio/swissknife: Handy code shared in the FMI CompBio group

Plot annotated phasogram.

Description

Plot phasogram and annotate it with estimated nucleosome repeat length (NRL).

Usage

plotPhasogram(x, hide = TRUE, xlim = NULL, verbosePlot = FALSE, ...)

Arguments

x	numeric vector giving the counts of alignment distances (typically the output of calcPhasogram.
hide	If TRUE (the default), hide phasogram counts not used in the NRL estimate (mind parameter from estimateNRL).
xlim	numeric(2) with the x-axis (phase) limits in the first two plots (see Details). if NULL (the default), the full range defined by x and hide will be used.
verbosePlot	If TRUE, create three plots instead of just a single plot (see Details).
...	Additional arguments passed to estimateNRL to control NRL estimation.

Details

The function will visualize an annotated phasogram. For verbosePlot=FALSE (the default), it will create a single annotated plot. For verbosePlot=TRUE, it will create three plots (using par(mfrow=c(1,3))):

1. raw phase counts with de-trending and de-noising loess fits

2. residual phase counts with de-noising loess fit and detected peaks

3. linear fit to peaks and NRL estimation

Value

The return value from the call to estimateNRL (invisibly).

Author(s)

Michael Stadler

See Also

calcPhasogram to calculate the phasogram from alignments, estimateNRL to estimate nucleosome repeat length

Examples

  # see the help for calcPhasogram() for a full example

fmicompbio/swissknife documentation built on June 11, 2025, 4:17 p.m.