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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")