plotAlignments: Plot alignments with respect to a reference sequence

Description Usage Arguments Value Author(s) See Also Examples

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

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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

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

CrispRVariants documentation built on Nov. 8, 2020, 11:09 p.m.