plotProfile: A function to generate a Vplot along chromosome coordinates

Description Usage Arguments Value Examples

View source: R/vplot-chroms.R

Description

A function to generate a Vplot along chromosome coordinates

Usage

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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

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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.