plotInflectionPoints {Scale4C} | R Documentation

## Draw a smoothed near-cis profile with marked inflection points for a 4C-seq signal

### 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)

[Package Scale4C version 1.6.0 Index]