plotEpibed: Plot the results of tabulateEpibed() as a quasi-lollipop...

In huishenlab/bisplotti: Plotting package for bisulfite sequencing data

Plot the results of tabulateEpibed() as a quasi-lollipop plot.

Description

NOTE: If you run tabulateEpibed() in NOMe mode with include_empty_reads = TRUE, then it is highly suggested you run plotEpibed() with show_all_points = TRUE also. If not, it is possible that reads in the CG and GC plots will not line up, depending on if there are empty reads in one plot, but not the other.

Usage

plotEpibed(
  mat,
  plot_meth_avg = FALSE,
  show_readnames = TRUE,
  show_positions = TRUE,
  show_all_points = FALSE,
  show_legend = TRUE,
  meth_color = "#FF2400",
  unmeth_color = "#6495ED",
  na_color = "grey",
  size = 6,
  n_reads = 20,
  n_loci = 10,
  force = FALSE
)

Arguments

mat	Input matrix that comes out of tabulateEpibed()
plot_meth_avg	Whether to also plot the average methylation state (default: FALSE)
show_readnames	Whether to show the read names (default: TRUE)
show_positions	Whether to show the genomic positions (default: TRUE)
show_all_points	Whether to show all points (i.e., empty reads, unknown, and filtered sites) (default: FALSE)
show_legend	Whether to include legend in plots (default: TRUE)
meth_color	What color should the methylated states be (default: '#FF2400')
unmeth_color	What color should the unmethylated states be (default: '#6495ED')
na_color	What color should the NA values be (default: 'grey')
size	What size the points should be drawn as (default: 6)
n_reads	Maximum number of reads to plot, if force = FALSE then takes first n_reads (default: 20)
n_loci	Maximum number of loci to plot, if force = FALSE then takes first n_loci (default: 10)
force	Force plotting of all reads and loci in input table (default: FALSE)

Value

An epibed ggplot object or list of ggplot objects if plot_read_avg is TRUE

Examples

epibed.nome <- system.file("extdata", "hct116.nome.epibed.gz",
                           package="biscuiteer")
epibed.nome.gr <- readEpibed(epibed = epibed.nome, is.nome = TRUE,
                             genome = "hg19", chr = "chr1")
epibed.tab.nome <- tabulateEpibed(epibed.nome.gr)
plotEpibed(epibed.tab.nome$gc_table)

huishenlab/bisplotti documentation built on Sept. 20, 2023, 10:13 p.m.