The paired-end fragments overlapping a locus of interest (e.g., binding sites, provided in the `loci` argument) are shown in red while the remaining fragments mapping to the genomic window are displayed in black. Marginal curves are also plotted on the side of the distribution plot. They highlight the smoothed distribution of the position of paired-end fragment midpoints (top) or of the paired-end fragment length (right)

plotProfile(
  fragments,
  window = loc,
  loci = NULL,
  annots = NULL,
  min = 50,
  max = 200,
  alpha = 0.5,
  size = 1,
  with_densities = TRUE,
  verbose = TRUE
)

Arguments

fragments

GRanges

window

character, chromosome location

loci

GRanges, optional genomic locus. Fragments overlapping this locus will be in red.

annots

GRanges, optional gene annotations

min

integer, minimum fragment size

max

integer, maximum fragment size

alpha

float, transparency value

size

float, dot size

with_densities

Boolean, should the densities be plotted?

verbose

Boolean

Value

A ggplot

Examples

data(bam_test) data(ce11_proms) V <- plotProfile( bam_test, 'chrI:10000-12000', loci = ce11_proms, min = 80, max = 200 )
#> Filtering and resizing fragments
#> 505 fragments mapped over 2001 bases
#> Filtering and resizing fragments
#> Generating plot
#> Warning: Removed 49 row(s) containing missing values (geom_path).
#> Warning: Removed 12 rows containing missing values (geom_point).
#> Warning: Removed 19 row(s) containing missing values (geom_path).