plot_agg_genes: Plot gene aggregate plot

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

Plot gene aggregate plot

Description

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)

Shians/NanoMethViz documentation built on May 24, 2024, 4:11 a.m.