View source: R/methMatrixManipulation.R
plotSingleMoleculesWithAvr | R Documentation |
Single molecule plot of a methylation matrix with average methylation frequency
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 )
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). |
A ggplot2 plot object
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