plotAlignments: Plot alignments with respect to a reference sequence

In HLindsay/CrispRVariants: Tools for counting and visualising mutations in a target location

Description

(signature("CrisprSet")) Wrapper for CrisprSet$plotVariants. Optionally filters a CrisprSet frequency table, then plots variants. More information in CrisprSet

(signature("DNAString")) Plots a set of pairwise alignments to a reference sequence. Alignments should all be the same length as the reference sequences. This is achieved by removing insertions with respect to the reference, see seqsToAln. Insertions are indicated by symbols in the plot and a table showing the inserted sequences below the plot. The default options are intended for a figure 6-8 inches wide, with figure height best chosen according to the number of different variants and insertions to be displayed.

Usage

plotAlignments(obj, ...)

## S4 method for signature 'CrisprSet'
plotAlignments(obj, ..., min.freq = 0, min.count = 1,
  top.n = 50, renumbered = obj$pars[["renumbered"]], add.other = TRUE,
  create.plot = TRUE)

## S4 method for signature 'character'
plotAlignments(obj, ..., alns, ins.sites,
  highlight.pam = TRUE, show.plot = FALSE, target.loc = 17,
  pam.start = NA, pam.end = NA, ins.size = 2, legend.cols = 3,
  xlab = NULL, xtick.labs = NULL, xtick.breaks = NULL,
  plot.text.size = 2, axis.text.size = 8, legend.text.size = 6,
  highlight.guide = TRUE, guide.loc = NULL, tile.height = 0.55,
  max.insertion.size = 20, min.insertion.freq = 5, line.weight = 1,
  legend.symbol.size = ins.size, add.other = FALSE, codon.frame = NULL,
  style = c("all", "mismatches"))

## S4 method for signature 'DNAString'
plotAlignments(obj, ..., alns, ins.sites,
  highlight.pam = TRUE, show.plot = FALSE, target.loc = 17,
  pam.start = NA, pam.end = NA, ins.size = 2, legend.cols = 3,
  xlab = NULL, xtick.labs = NULL, xtick.breaks = NULL,
  plot.text.size = 2, axis.text.size = 8, legend.text.size = 6,
  highlight.guide = TRUE, guide.loc = NULL, tile.height = 0.55,
  max.insertion.size = 20, min.insertion.freq = 5, line.weight = 1,
  legend.symbol.size = ins.size, add.other = FALSE, codon.frame = NULL)

Arguments

obj	The object to be plotted
...	Additional arguments
min.freq	i ( one sample (default: 0, i.e no frequency cutoff)
min.count	i (integer) only plot variants with count >= i in at least one sample (default: 0, i.e no count cutoff)
top.n	(integer) Plot only the n most frequent variants (default: 50)
renumbered	If TRUE, the x-axis is numbered with respect to the target (default: TRUE)
add.other	Add a blank row labelled "Other" to the plot, for combining with plotFreqHeatmap (default: TRUE (signature "CrisprSet") FALSE (signature "matrix"))
create.plot	Should the data be plotted? If false, returns the data used for plotting (Default: TRUE)
alns	A named character vector of aligned sequences, with insertions removed
ins.sites	A table of insertion_sites, which must include cols named "start", "cigar", "seq" and "count" for the start of the insertion in the corresponding sequence
highlight.pam	should location of PAM with respect to the target site be indicated by a box? (Default: TRUE) If TRUE, and pam.start and pam.end are not supplied, PAM is inferred from target.loc
show.plot	Should the plot be displayed (TRUE) or just returned as a ggplot object (FALSE). (Default: FALSE)
target.loc	The location of the zero point / cleavage location. Base n, where the zero point is between bases n and n+1
pam.start	The first location of the PAM with respect to the reference.
pam.end	The last location of the PAM with respect to the reference. Default is two bases after the pam.start
ins.size	The size of the symbols representing insertions within the plot.
legend.cols	The number of columns in the legend. (Default:3)
xlab	A title for the x-axis (Default: NULL)
xtick.labs	Labels for the x-axis ticks (Default: NULL)
xtick.breaks	Locations for x-axis tick breaks (Default: NULL)
plot.text.size	The size of the text inside the plot
axis.text.size	The size of the axis labels
legend.text.size	The size of the legend labels
highlight.guide	Should the guide be indicated by a box in the reference sequence? (Default: TRUE)
guide.loc	The location of the guide region to be highlighted, as an IRanges object. Will be inferred from target.loc if highlight.guide = TRUE and no guide.loc is supplied, assuming the guide plus PAM is 23bp (Default: NULL)
tile.height	The height of the tiles within the plot. (Default: 0.55)
max.insertion.size	The maximum length of an insertion to be shown in the legend. If max.insertion.size = n, an insertion of length m > n will be annotated as "mI" in the figure. (Default: 20)
min.insertion.freq	Display inserted sequences with frequency at least x amongst the sequences with an insertion of this size and length (Default: 5)
line.weight	The line thickness for the vertical line indicating the zero point (cleavage site) and the boxes for the guide and PAM. (Default: 1)
legend.symbol.size	The size of the symbols indicating insertions in the legend. (Default: ins.size)
codon.frame	Codon position of the leftmost nucleotide. If provided, codon positions in the specified frame are indicated. (Default: NULL)
style	One of "all" (colour all tiles) and "mismatches" (colour only mismatch positions)

Value

A ggplot2 figure

Author(s)

Helen Lindsay

See Also

seqsToAln, ggplot

Examples

#Load a CrisprSet object and plot
data("gol_clutch1")
plotAlignments(gol)

HLindsay/CrispRVariants documentation built on May 28, 2019, 12:40 p.m.