manhattan_plot Manhattan plot showing on/off-targets detected organized by chromosomal position with bar height representing read count (number of breaks).

manhattan_plot Manhattan plot showing on/off-targets detected organized by chromosomal position with bar height representing read count (number of breaks).

Usage

manhattan_plot(
  x,
  bsgenome,
  standard_chromosomes = TRUE,
  cutsite_breaks_only = TRUE,
  subtract_nontarget = FALSE,
  log_signal = FALSE,
  verbose = TRUE
)

Arguments

x

A GRanges object containing the results of a breakinspectoR analysis. Possibly filtered (eg. qval < .01).

bsgenome

character, bsgenome to use (eg. BSgenome.Hsapiens.UCSC.hg38).

standard_chromosomes

logical, constrain the analysis to standard. chromosomes only. Default: TRUE.

cutsite_breaks_only

display breaks of cutsite only, instead of using breaks accumulated in the complete protospacer. Default: TRUE

subtract_nontarget

subtract breaks of non-target library. Default: FALSE

log_signal

display log2 transformed signal. Default: FALSE.

verbose

logical, keep informing about every step.

Value

A ggplot object.

Examples

if (FALSE) { # \dontrun{
  offtargets <- breakinspectoR(
    target   =system.file("extdata/vegfa.chr6.bed.gz", package="breakinspectoR"),
    nontarget=system.file("extdata/nontarget.chr6.bed.gz", package="breakinspectoR"),
    guide    ="GACCCCCTCCACCCCGCCTC",
    PAM      =c("NGG", "NAG"),
    bsgenome ="BSgenome.Hsapiens.UCSC.hg38",
    cutsiteFromPAM=3
  )
} # }
data(breakinspectoR_examples)

manhattan_plot(
  offtargets,
  bsgenome ="BSgenome.Hsapiens.UCSC.hg38"
)
#> Loading BSgenome.Hsapiens.UCSC.hg38...
#>  done