plotMutability - Plot mutability probabilities
plotMutability plots the mutability rates of a
plotMutability(model, nucleotides = c("A", "C", "G", "T"), mark = NULL, style = c("hedgehog", "bar"), size = 1, silent = FALSE, ...)
- TargetingModel object or vector containing normalized mutability rates.
- vector of center nucleotide characters to plot.
- vector of 5-mer motifs to highlight in the plot. If
NULLonly highlight classical hot and cold spot motifs.
- type of plot to draw. One of:
"hedgehog": circular plot showing higher mutability scores further from the circle. The 5-mer is denoted by the values of the inner circle. The 5-mer is read from the most interior position of the 5-mer (5’) to most exterior position (3’), with the center nucleotide in the center ring. Note, the order in which the 5-mers are plotted is different for nucleotides
"bar": bar plot of mutability similar to the
hedgehogstyle with the most 5’ positions of each 5-mer at the base of the plot.
- numeric scaling factor for lines and text in the plot.
TRUEdo not draw the plot and just return the ggplot2 objects; if
FALSEdraw the plot.
- additional arguments to pass to ggplot2::theme.
A named list of ggplot objects defining the plots, with names defined by the center nucleotide for the plot object.
# Plot one nucleotide in circular style plotMutability(HH_S5F, "C")
# Plot two nucleotides in barchart style plotMutability(HH_S5F, c("G", "T"), style="bar")