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())

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