plot_agg_regions: Plot aggregate regions

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

Plot aggregate regions

Description

Plot aggregate regions

Usage

plot_agg_regions(
  x,
  regions,
  binary_threshold = 0.5,
  group_col = NULL,
  flank = 2000,
  stranded = TRUE,
  span = 0.05,
  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).
flank	the number of flanking bases to add to each side of each region.
stranded	TRUE if negative strand features should have coordinates flipped to reflect features like transcription start sites.
span	the span for loess smoothing.
palette	the ggplot colour palette used for groups.

Value

a ggplot object containing the aggregate methylation trend.

Examples

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

Shians/NanoMethViz documentation built on May 19, 2024, 7:18 a.m.