plot_intervals {multicrispr} | R Documentation |
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" )
gr |
|
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 |
ggplot object
# 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())