plotFinalClasses: Plot reads and class means with final classification

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

Plot reads and class means with final classification

Description

Plot reads and class means with final classification

Usage

plotFinalClasses(
  dataOrderedByClass,
  numClasses,
  allClassMeans,
  outFileBase,
  outPath,
  xRange,
  myXlab,
  featureLabel,
  baseFontSize,
  figFormat = "png",
  classesToPlot = NULL
)

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.
numClasses	An integer indicating the number of classes to learn
allClassMeans	A long data frame of methylation or bincount values with columns for position, methylation frequency (methFreq), class and replicate.
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
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)
figFormat	format of output figures. Should be one of "png" or "pdf"
classesToPlot	A numerical vector indicating which classes to plot (default NULL will plot all classes)

Value

None

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