plotProfile: A function to generate a Vplot along chromosome coordinates

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

Description

A function to generate a Vplot along chromosome coordinates

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
)

VplotR documentation built on Nov. 8, 2020, 7:50 p.m.