methylation_global_distribution: Global methylation distribution

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Global methylation distribution

Usage

methylation_global_distribution(sample_id, subgroup,
    reorder_column = TRUE,
    ha = HeatmapAnnotation(subgroup = subgroup, show_annotation_name = TRUE),
    chromosome = paste0("chr", 1:22), by_chr = FALSE,
    background = NULL, p = NULL, meth_range = c(0, 1),
    max_cov = 100, plot_cov = FALSE)

Arguments

sample_id	a vector of sample IDs
subgroup	subgroup information
reorder_column	if it is true, samples are first ordered by subgroups and in each subgroup, samples are ordered by median values
ha	Annotations that are specified as a HeatmapAnnotation-class object. The annotations will be put on top of the heatmap.
chromosome	chromosome names
by_chr	whether make the plot by chromosome
background	background to look into. The value can be a single GRanges object or a list of GRanges objects.
p	probability to randomly sample CpG sites
meth_range	the range of methylation on the plot
max_cov	maximum range for coverage
plot_cov	whether also make plot for coverage

Details

There are two types of plots:

• a heatmap showing the distribution density of methylation in all samples

• a MDS plot

Value

If by_chr is set to FALSE, it returns a vector of column order.

Author(s)

Zuguang Gu <[e-mail]>

See Also

It uses mat_dist to make the plots

Examples

# There is no example
NULL

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.