plotMutability {shazam}

Plot mutability probabilities

Description

plotMutability plots the mutability rates of a TargetingModel.

Usage

plotMutability(
  model,
  nucleotides = c("A", "C", "G", "T"),
  mark = NULL,
  style = c("hedgehog", "bar"),
  size = 1,
  silent = FALSE,
  ...
)

Arguments

model

TargetingModel object or vector containing normalized mutability rates.

nucleotides

vector of center nucleotide characters to plot.

mark

vector of 5-mer motifs to highlight in the plot. If NULL only highlight classical hot and cold spot motifs.

style

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 c("A", "C") and c("G", "T").

• "bar": bar plot of mutability similar to the hedgehog style with the most 5' positions of each 5-mer at the base of the plot.

size

numeric scaling factor for lines and text in the plot.

silent

if TRUE do not draw the plot and just return the ggplot2 objects; if FALSE draw the plot.

...

additional arguments to pass to ggplot2::theme.

Value

A named list of ggplot objects defining the plots, with names defined by the center nucleotide for the plot object.

See Also

Takes as input a TargetingModel object. See createTargetingModel for model building.

Examples

# Plot one nucleotide in circular style
plotMutability(HH_S5F, "C")

# Plot two nucleotides in barchart style
plotMutability(HH_S5F, c("G", "T"), style="bar")