plotAlignments {CrispRVariants} | R Documentation

## Plot alignments with respect to a reference sequence

### 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)

[Package CrispRVariants version 1.8.0 Index]