plot_violin: Plot violin for regions

In Shians/NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing

Plot violin for regions

Description

This function plots a violin plot of the methylation proportion for each region in the regions table. The methylation proportion is calculated as the mean of the modification probability wihtin each region and the violin represents the . The regions are then grouped and coloured by the group_col column in the regions table or samples(x).

Usage

plot_violin(
  x,
  regions,
  binary_threshold = 0.5,
  group_col = "group",
  palette = ggplot2::scale_colour_brewer(palette = "Set1")
)

Arguments

x	the NanoMethResult object.
regions	a table of regions containing at least columns chr, strand, start and end. Any additional columns can be used for grouping.
binary_threshold	the modification probability such that calls with modification probability above the threshold are considered methylated, and those with probability equal or below are considered unmethylated.
group_col	the column to group aggregated trends by. This column can be in from the regions table or samples(x).
palette	the ggplot colour palette used for groups.

Value

a ggplot object containing the methylation violin plot.

Examples

nmr <- load_example_nanomethresult()
gene_anno <- exons_to_genes(NanoMethViz::exons(nmr))
plot_violin(nmr, gene_anno)
plot_violin(nmr, gene_anno, group_col = "sample")

Shians/NanoMethViz documentation built on Dec. 17, 2024, 8:56 a.m.