plotTraceback: Draw the traceback results for a list of singular points on a...

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

Description

This method plots the traceback results together with fingerprint data, allowing to check for possible errors during tracking. Problems during tracking can occur if contours are very close, have holes, or if the singularity in question is not recognized at all due to holes at the meeting point of both contours that form a singular point. Each singular point is marked with a grey triangle, and the traced left and right end of the corresponding feature are connected with grey lines. If a contour's end doesn't match the traceback line, manual correction is possible in the singularity list.

Usage

plotTraceback(data, maxSQSigma = -1, fileName = "tracebackPlot.pdf", 
width = 15, height = 15, useIndex = TRUE)

Arguments

data	Scale4C object with singularity data
maxSQSigma	Maximum square sigma (i.e. maximum y value) to be drawn; if -1 then all available rows in the fingerprint map are used
fileName	Optional name for export file (pdf)
width	Width of the plot
height	Height of the plot
useIndex	If TRUE, use fragment index for x-axis

Value

A traceback plot, showing the traced singular points with their points of origin throughout different smoothing layers)

Note

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

Author(s)

Carolin Walter

Examples

    if(interactive()) {
        data(liverData)
        plotTraceback(liverData)
    }

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