plotEachRepeat: Plot single molecule and class means for individual repeats

In jsemple19/EMclassifieR: Classify DSMF data using the Expectation Maximisation algorithm

Plot single molecule and class means for individual repeats

Description

Plot single molecule and class means for individual repeats

Usage

plotEachRepeat(
  dataOrderedByClass,
  outFileBase,
  outPath,
  numClasses,
  EMrep,
  classMeans,
  xRange,
  myXlab,
  featureLabel,
  baseFontSize
)

Arguments

dataOrderedByClass	A matrix of methylation or bincount values (reads x position) that have been ordered by class. The assigned class, e.g. "__class1" etc has been appended to read names.
outFileBase	A string that will be used in the filenames and titles of the plots produced
outPath	path to directory where plots will be saved
numClasses	An integer indicating the number of classes to learn
EMrep	An integer indicating which repeat of the EM this is
classMeans	A matrix (classes x position) of the average methlyation profile of each class classes
xRange	A vector of the first and last coordinates of the region to plot (default is c(-250,250))
myXlab	A label for the x axis (default is "CpG/GpC position")
featureLabel	A label for a feature you want to plot, such as the position of the TSS (default="TSS")
baseFontSize	The base font for the plotting theme (default=12 works well for 4x plots per A4 page)

Value

Returns a ggplot2 object

jsemple19/EMclassifieR documentation built on Aug. 12, 2022, 2:57 p.m.