Interval plot GRanges

Interval plot GRanges

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)
#> 	Read SRF.bed into GRanges
#> 		1974 ranges on 21 chromosomes
    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)
#> Find primespacers for 4 targets
#> 	Found 10 primespacers
#> 	Count offtargets with max 0 mismatches using bowtie
#> 		Count genome (mis)matches
#> 			Expand iupac ambiguities in pam
#> 			Write reads to ~/multicrisprout/spacers.fa
#> 			Map reads: ~/multicrisprout/spacers/spacers_to_BSgenome.Hsapiens.UCSC.hg38.txt
#> 			Load results
#> 				Read 53 hits with max 1 mismatch(es)
#> 				Retain 20 after removing NGG 'N' mismatches (avoid double counting expanded pams)
#> 				Retain 20 after removing NGG 'G1' mismatches(except for NGG -> NAG, which is allowed)
#> 				Retain 20 after removing NGG 'G2' mismatches
#> 				Retain 11 after removing more than 0 mismatches
#> 			Count matches
#> 		Count off-targets
#> 		       9 are off0 free
#> 	Score ontargets
#> 		Add (4-23-3) contextseqs
#> 		Score contextseqs with Doench2014
#> Find nickspacers
#> Find spacers in 10 targets
#> 	Found 32 spacers
#> 	Count offtargets with max 2 mismatches using bowtie
#> 		Count genome (mis)matches
#> 			Expand iupac ambiguities in pam
#> 			Write reads to ~/multicrisprout/spacers.fa
#> 			Map reads: ~/multicrisprout/spacers/spacers_to_BSgenome.Hsapiens.UCSC.hg38.txt
#> 			Load results
#> 				Read 91 hits with max 2 mismatch(es)
#> 				Retain 37 after removing NGG 'N' mismatches (avoid double counting expanded pams)
#> 				Retain 36 after removing NGG 'G1' mismatches(except for NGG -> NAG, which is allowed)
#> 				Retain 33 after removing NGG 'G2' mismatches
#> 				Retain 33 after removing more than 2 mismatches
#> 			Count matches
#> 		Count off-targets
#> 		       30 are off0 free
#> 		       32 are off1 free
#> 		       24 are off2 free
#> 	Filter for best offtarget counts
#> 		Retain 32 with best off0 counts per pename
#> 		Retain 32 with best off1 counts per pename
#> 		Retain 24 with best off2 counts per pename
#> 	Score ontargets
#> 		Add (4-23-3) contextseqs
#> 		Score contextseqs with Doench2014
    plot_intervals(gr)
    plot_intervals(extend_for_pe(gr))
    plot_intervals(spacers)
#> Warning: Removed 34 rows containing missing values (geom_point).
#> Warning: Removed 34 rows containing missing values (geom_point).

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