plot.LFRset: Plotting an LFR data set

In chedonat/DigitalPicoTools: DIGITAL ANALYSIS OF PICOGRAM QUANTITIES OF DNA

Description

This is a generic function to plot in different way the Length and the Average coverage of the long Frangment Reads within an LFR data set. Two type of plot can be performed.

ScatterPlot

this plot represent a scatter plot between the Length and the Average Coverage

Landscape

This plot type represent the distribution of the LFR across the whole genome. It adds a third dimension to the length and the coverage which is the genomic location.

Usage

## S3 method for class 'LFRset'
plot(object, type = "ScatterPlot", value = "Coverage",
  minlength = 10000, color = "black", main = "", well = NULL)

Arguments

type	the type of the plot. Can be either 'ScatterPlot' either 'Landscape'. The default value is 'ScatterPlot'.
minlength	Minimum length of a fragment to be considered. Default 10000.
color	The points color. default: black
main	The title of the plot. default: None
x	an LFRset object containing the list of Long Fragment Reads
Value	The variable to represent on the y-Axis. Can be either 'Coverage' either 'length'. default is 'Coverage'.

Details

In both types, the paramater Value allow to specifie which variable will be represented on the y-axis. It can be 'Coverage' for the LFR Average Coverage and 'Length' for the LFR lengths.

Value

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See Also

plotLFRDistribution, plot.LFRset, getWells, getWellLFRset, getLFRStats

Examples

 #Example 1:
 wellsID_file=system.file('extdata','wells_id_tissue.txt',package='DigitalPicoTools')
 wellsID_list<-unlist(read.table(wellsID_file))
 WellSample_list=initsWellSamples(wellsID_list,
     BAMprefix=paste(path.package('DigitalPicoTools'),'extdata/',sep='/'))
 LFR_Info = getLFRset(WellSample_list,3000)
 well1=getWellLFRset(LFR_Info,1)
 plot(well1,value='Length')
 plot(LFR_Info,type='Landscape', color='magenta',main='test')
 plot(well1,value='Coverage',type='Landscape')

chedonat/DigitalPicoTools documentation built on May 13, 2019, 3:39 p.m.