plot_intervals {multicrispr} | R Documentation

## Interval plot GRanges

### Description

Interval plot GRanges

### Usage

    plot_intervals(
      gr,
      xref = "targetname",
      y = default_y(gr),
      nperchrom = 2,
      nchrom = 4,
      color_var = "targetname",
      facet_var = "seqnames",
      linetype_var = default_linetype(gr),
      size_var = default_size_var(gr),
      alpha_var = default_alpha_var(gr),
      title = NULL,
      scales = "free"
    )

### Arguments

`gr` | `GRanges-class`
`xref` | gr var used for scaling x axis
`y` | 'names' (default) or name of gr variable
`nperchrom` | number (default 1): n head (and n tail) targets shown per chromosome
`nchrom` | number (default 6) of chromosomes shown
`color_var` | 'seqnames' (default) or other gr variable
`facet_var` | NULL(default) or gr variable mapped to facet
`linetype_var` | NULL (default) or gr variable mapped to linetype
`size_var` | NULL (default) or gr variable mapped to size
`alpha_var` | NULL or gr variable mapped to alpha
`title` | NULL or string: plot title
`scales` | 'free', 'fixed', etc

### Value

ggplot object

### See Also

`plot_karyogram`

### Examples

    # SRF sites
        require(magrittr)
        bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
        bedfile <-  system.file('extdata/SRF.bed',  package = 'multicrispr')
        targets   <- bed_to_granges(bedfile, 'mm10', plot = FALSE)
        plot_intervals(targets)

    # PE targets
        bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
        gr <- char_to_granges(c(PRNP = 'chr20:4699600:+',
                                HBB  = 'chr11:5227002:-',
                                HEXA = 'chr15:72346580-72346583:-',
                                CFTR = 'chr7:117559593-117559595:+'),
                              bsgenome)
        spacers <- find_primespacers(gr, bsgenome, plot = FALSE)
        plot_intervals(gr)
        plot_intervals(extend_for_pe(gr))
        plot_intervals(spacers)

    # Empty gr
        plot_intervals(GenomicRanges::GRanges())

[Package multicrispr version 1.2.0 Index]