plotProfile: A function to generate a Vplot along chromosome coordinates

In js2264/VplotR: Set of tools to make V-plots and compute footprint profiles

A function to generate a Vplot along chromosome coordinates

Description

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)

Usage

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
)

js2264/VplotR documentation built on Jan. 4, 2024, 7:49 p.m.