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plotExpectedFootprint

Source: R/plots.R
plotExpectedFootprint.Rd

Creates a footprint plot of expected vs observed methylation for a given motif and a single methylation site.

Usage

plotExpectedFootprint(
  motif,
  tf_bindsites,
  msites,
  sample_name = NULL,
  gc_dist,
  gcfreqs,
  enhancer = NULL,
  returnPlotData = FALSE
)

Arguments

motif

Motif name as a character string

tf_bindsites

Transcript Factor binding sites from the annotation package

msites

Methylation sites as a data frame

sample_name

Optional sample name as a character string, defaults to the file name if not provided

gc_dist

a GRanges object contains Genome wide GC distribution

gcfreqs

GC frequency of the genome used to compute expected methylation

enhancer

Specific region such as distal motif, proximal motif

returnPlotData

Logical indicating whether to return the plot data

Value

A ggplot object of TF footprint plot for a single sample

Examples

library(ggplot2)
library(methylTFR)

# Load the data
load(system.file("extdata",
    "BATF_tf_bindsites.rda",
    package = "methylTFR"
))
load(system.file("extdata",
    "example_data.rda",
    package = "methylTFR"
))
load(system.file("extdata",
    "BATF_gcfreqs.rda",
    package = "methylTFR"
))
load(system.file("extdata",
    "gcdist_subset.rda",
    package = "methylTFR"
))

# Plot the expected footprint
p <- plotExpectedFootprint(
    motif = "BATF",
    tf_bindsites = tf_bindsites,
    msites = msites,
    sample_name = "Sample1",
    gc_dist = gcdist,
    gcfreqs = gcfreqs,
    enhancer = NULL,
    returnPlotData = FALSE
)