plot_infer_profiles: Plot inferred methylation profiles across a region

In andreaskapou/BPRMeth: Model higher-order methylation profiles

Description

Function for plotting the inferred methylation profiles across a given region, and optionally the mean methylation rate together with the observed methylation data, using ggplot2.

Usage

plot_infer_profiles(
  region = 1,
  obj_prof,
  obj_mean = NULL,
  obs = NULL,
  title = "Inferred profiles",
  x_axis = "genomic region",
  y_axis = "met level",
  x_labels = c("Upstream", "", "Centre", "", "Downstream"),
  ...
)

Arguments

region	Genomic region number
obj_prof	Inferred profile, i.e. output from infer_profiles_vb or infer_profiles_mle
obj_mean	Inferred mean function, i.e. output from infer_profiles_vb or infer_profiles_mle
obs	Methylation data observations, if a list, will extract the specific region, if a matrix will plot directly its observations.
title	Plot title
x_axis	x axis label
y_axis	x axis label
x_labels	x axis ticks labels
...	Additional parameters

Value

A ggplot2 object.

Author(s)

C.A.Kapourani [e-mail]

See Also

plot_predicted_expr, plot_cluster_profiles, boxplot_cluster_expr

Examples

# Fit methylation profiles using 5 RBFs
basis <- create_rbf_object(M = 5)
prof <- infer_profiles_vb(X = encode_met$met, model = "binomial",
    basis = basis, is_parallel = FALSE, vb_max_iter = 5)
# Create the plot
g <- plot_infer_profiles(region = 16, obj_prof = prof, obs = encode_met$met)

andreaskapou/BPRMeth documentation built on June 11, 2020, 10:49 p.m.