plotTesselation: Draw the final scale space tesselation

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

Description

This method draws the final scale space tesselation, as specified by the list of singularities identified for a Scale4C object. Features are marked with different colours; for the default colour scheme, brown corresponds to 'peaks' and blue to 'valleys', while slightly darker colours mark features originating from singularities ('central' features in a set of three features, e.g. 'valley-peak-valley' or 'peak-valley-peak') and lighter colours the two adjacent features. Different colours for 'central' and 'adjacent' features allow for optical quality control of the tesselation: a 'central' / dark feature's direct predecessor or successor (y-axis) can't be of the same colour (i.e. a 'peak' that passes through a singularity is smoothed out into a 'valley'), and neighbouring intervals have to be of the opposing (but lighter) colour (i.e. each 'peak' is surrounded by two 'valleys' for Gauss kernel smoothing). The same is not necessarily true for an 'adjacent' / light feature, however.

Usage

plotTesselation(data, minSQSigma = 5, maxSQSigma = -1, maxVis = -1, 
fileName = "tesselationPlot.pdf", width = 5, height = 5, xInterval = 100, 
yInterval = 50, chosenColour = c("grey50", "moccasin", "lightskyblue1", 
"beige", "azure"), useIndex = TRUE)

Arguments

data	Scale4C object with singularity data
minSQSigma	Minimum square sigma to consider
maxSQSigma	Maximum square sigma to consider; if -1 then the number of rows in the fingerprint map is used
maxVis	Maximum y value for visualization (doesn't have to be maxSQSigma); if -1 also defaults to number of rows in the fingerprint map
fileName	Optional name for export file (pdf)
width	Width of the plot
height	Height of the plot
xInterval	Interval length for x-axis
yInterval	Interval length for y-axis
chosenColour	Chosen colours for the tesselation plot, five in total. Colour 1 is used for the actual lines of the plot, colour 2 for 'central peaks', colour 3 for 'central valleys', colour 4 for 'adjacent peaks', and colour 5 for 'adjacent valleys'
useIndex	If TRUE, use fragment index for x-axis

Value

A tesselation plot, showing different features of the scale space with their range of existance (square sigma) and position)

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)
        plotTesselation(liverData)
    }

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