A function to generate a Vplot along chromosome coordinates

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 rows containing missing values (`geom_line()`).
#> Warning: Removed 12 rows containing missing values (`geom_point()`).
#> Warning: Removed 19 rows containing missing values (`geom_line()`).