AlleleProfileR.plot.alignment: Alignment plot function

In abruyneel/AlleleProfileR: Genome editing strategy agnostic variant identification and profiling tool

Description

THis function plots sequence alignments.

Usage

AlleleProfileR.plot.alignment(config, sample.id = NA, gene.id = NA,
  max.insertion.size = 20, ins.size = 5,
  legend.symbol.size = ins.size, legend.text.size = 6,
  plot.text.size = 2, axis.text.size = 8, alternate = NULL,
  alignmenttype = "local-global")

Arguments

config	Configuration list, as generated by AlleleProfileR.setup.
sample.id	Sample id, from samples object.
gene.id	Gene id, from genes table.
max.insertion.size	The maximum length of an insertion to be shown in the legend. Larger insertions will be collapsed. Default is 20.
ins.size	The size of the symbols representing insertions within the plot. Default is 5.
legend.symbol.size	The size of the symbols indicating insertions in the legend. Default is ins.size.
legend.text.size	The size of the legend labels. Default is 6.
plot.text.size	The size of the text inside the plot. Default is 2.
axis.text.size	The size of the axis labels. Default is 8.
alternate	Alternate reference for labeling the HDR variant, as defined by AlleleProfileR.alternatereference.
alignmenttype	Type for Biostrings::pairwiseAlignment operation to determine whether two alleles are identical. Default is "local-global".

Value

Alignment plot

Author(s)

Arne Bruyneel

References

This function incorporates some of the plotting features of CrispRVariants (Helen Lindsay).

• Lindsay H, Burger A, Biyong B, Felker A, Hess C, Zaugg J, Chiavacci E, Anders C, Jinek M, Mosimann C, Robinson MD. CrispRVariants charts the mutation spectrum of genome engineering experiments. Nature Biotechnology 2016;34:701–702. doi: 10.1038/nbt.3628.

abruyneel/AlleleProfileR documentation built on June 12, 2020, 2:47 p.m.