plotInflectionPoints: Draw a smoothed near-cis profile with marked inflection...

In Scale4C: Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

Description

plotInflectionPoints plots the inflection points for a given square sigma (i.e. a row of the fingerprint map) onto a corresponding smoothed near-cis plot for the 4C-seq signal. This allows to check problematic parts of the fingerprint map in more detail (e.g. unclear tracking areas with close contours), and to improve possible corrections in the singularity list. Plotting the smoothed signal for a given square sigma before calculation of the fingerprint map is also possible.

Usage

plotInflectionPoints(data, sqsigma, fileName = "inflectionPlot.pdf", 
width = 9, height = 5, maxVis = 5000, useIndex = TRUE, plotIP = TRUE)

Arguments

data	Scale4C object with experimental 4C-seq data to be smoothed and processed
sqsigma	Chosen square sigma, i.e. row of the fingerprint map to pick the inflection points from
fileName	Optional name for export file (pdf)
width	Width of the plot
height	Height of the plot
maxVis	Maximum y-axis value (read number, not sigma!) for visualization
useIndex	If TRUE, use fragment index for x-axis
plotIP	If TRUE, then mark chosen inflection points, if FALSE, simply plot smoothed data

Value

A near-cis plot of the smoothed data with (optional) marked inflection points in darker or lighter grey, depending on their direction

Note

PDF export is supported. If no plot file name is provided, the result is plotted on screen.

Author(s)

Carolin Walter

Examples

    data(liverData)
    plotInflectionPoints(liverData, 50)

Scale4C documentation built on Nov. 8, 2020, 8:21 p.m.