plot_region_heatmap: Plot region methylation heatmap

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

Plot region methylation heatmap

Description

Plot the methylation heatmap of a genomic region.

Usage

plot_region_heatmap(x, chr, start, end, ...)

## S4 method for signature 'NanoMethResult,character,numeric,numeric'
plot_region_heatmap(
  x,
  chr,
  start,
  end,
  pos_style = c("to_scale", "compact"),
  window_prop = 0,
  subsample = 50
)

## S4 method for signature 'ModBamResult,character,numeric,numeric'
plot_region_heatmap(
  x,
  chr,
  start,
  end,
  pos_style = c("to_scale", "compact"),
  window_prop = 0,
  subsample = 50
)

## S4 method for signature 'NanoMethResult,factor,numeric,numeric'
plot_region_heatmap(
  x,
  chr,
  start,
  end,
  pos_style = c("to_scale", "compact"),
  window_prop = 0,
  subsample = 50
)

## S4 method for signature 'ModBamResult,factor,numeric,numeric'
plot_region_heatmap(
  x,
  chr,
  start,
  end,
  pos_style = c("to_scale", "compact"),
  window_prop = 0,
  subsample = 50
)

Arguments

x	the NanoMethResult or ModBamResult object.
chr	the chromosome to plot.
start	the start of the plotting region.
end	the end of the plotting region.
...	additional arguments.
pos_style	the style for plotting the base positions along the x-axis. Defaults to "to_scale", plotting (potentially) overlapping squares along the genomic position to scale. The "compact" options plots only the positions with measured modification.
window_prop	the size of flanking region to plot. Can be a vector of two values for left and right window size. Values indicate proportion of gene length.
subsample	the number of read of packed read rows to subsample to.

Value

a ggplot object of the heatmap.

a ggplot plot containing the heatmap.

Examples

nmr <- load_example_nanomethresult()
plot_region_heatmap(nmr, "chr7", 6703892, 6730431)

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