plotVariants {CrispRVariants} | R Documentation

## Plot alignments, frequencies and location of target sequence

### Description

Combines a plot of transcript structure, alleles aligned with respect to a reference genome and a heatmap of counts or proportions of each allele in a set of data.

### Usage

    plotVariants(obj, ...)

    ## S4 method for signature 'CrisprSet'
    plotVariants(obj, ..., txdb = NULL, add.chr = TRUE,
      plotAlignments.args = list(), plotFreqHeatmap.args = list())

### Arguments

`obj` | The object to be plotted
`...` | extra arguments for plot layout
`txdb` | GenomicFeatures:TxDb object (default: NULL)
`add.chr` | If target chromosome does not start with "chr", e.g. "chr5", add the "chr" prefix. (Default:TRUE)
`plotAlignments.args` | Extra arguments for plotAlignments
`plotFreqHeatmap.args` | Extra arguments for plotFreqHeatmap

### Value

A ggplot2 plot of the variants

### See Also

`arrangePlots` for general layout options and `annotateGenePlot` for options relating to the transcript plot.

### Examples

    #Load a CrisprSet object for plotting
    data("gol_clutch1")

    #Load the transcript db.  This is a subset of the Ensembl Danio Rerio v73 gtf
    # for the region 18:4640000-4650000 which includes the targeted gol gene

    library(GenomicFeatures)
    fn <- system.file("extdata", "Danio_rerio.Zv9.73.gol.sqlite",
                     package = "CrispRVariants")
    txdb <- loadDb(fn)

    # Plot the variants
    p <- plotVariants(gol, txdb = txdb)

    #In the above plot, the bottom margin is too large, the legend is
    #cut off, and the text within the plots should be larger.
    #These issues can be fixed with some adjustments:
    p <- plotVariants(gol, txdb = txdb,
                     plotAlignments.args = list(plot.text.size = 4, legend.cols = 2),
                     plotFreqHeatmap.args = list(plot.text.size = 4),
                     left.plot.margin = grid::unit(c(0.1,0,0.5,1), "lines"))

[Package CrispRVariants version 1.12.0 Index]