plotSingleMoleculesWithAvr: Single molecule plot of a methylation matrix with average...
In jsemple19/methMatrix: Manipulate Lists of Methylation Matrices

plotSingleMoleculesWithAvr

R Documentation

Single molecule plot of a methylation matrix with average methylation frequency

Description

Single molecule plot of a methylation matrix with average methylation frequency

Usage

plotSingleMoleculesWithAvr(
  mat,
  regionName,
  regionGRs,
  featureGRs,
  myXlab = "CpG/GpC position",
  featureLabel = "TSS",
  drawArrow = TRUE,
  title = NULL,
  baseFontSize = 11,
  maxNAfraction = 0.2,
  segmentSize = 3,
  colourChoice = list(low = "blue", mid = "white", high = "red", bg = "white", lines =
    "grey80"),
  colourScaleMidpoint = 0.5,
  doClustering = T
)

Arguments

`mat`	A methylation matrix
`regionName`	The name of the region the matrix is taken from should match on of the IDs in regionGRs
`regionGRs`	A genomicRanges object which includes the region which the mat matrix provides the data for. The object must contain a metadata column called "ID" containing names that match the methylation matrices in mat
`featureGRs`	A genomicRanges object denoting features to be plotted such as the TSS
`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)
`drawArrow`	Boolean: should the feature be drawn as an arrow or just a line? (default=TRUE)
`title`	A title for the plot (default will be the name of the region, the chr and strand on which the region is present)
`baseFontSize`	The base font for the plotting theme (default=11 works well for 4x plots per A4 page)
`maxNAfraction`	Maximual fraction of CpG/GpC positions that can be undefined (default=0.2)
`segmentSize`	Length of colour segment denoting methylation site
`colourChoice`	A list of colours for colour pallette. Must include values for "low", "mid", "high" and "bg" (background) and "lines".
`colourScaleMidpoint`	Numerical value for middle of colour scale. Useful for Nanopore data where a particular threshold other than 0.5 is used to distinguish methylated from non-methylated sites. (default=0.5).
`doClustering`	Boolean value to determine if reads should be clustered with heirarchical clustering before plotting (default=T).