Plot gene aggregate plot

Usage

plot_agg_genes(
  x,
  genes = NULL,
  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.
genes: a character vector of genes to include in aggregate plot, if NULL then all genes are used.
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 of genes.

Examples

nmr <- load_example_nanomethresult()
plot_agg_genes(nmr)