Plot region methylation heatmap

Plot the methylation heatmap of a genomic region.

Usage

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

# S4 method for class '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 class '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 class '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 class '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 region 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.

Details

This function creates a heatmap visualization of methylation data for a specified genomic region. Each row represents one or more packed reads, with colored segments indicating methylation probability at each position. Reads are packed vertically to minimize plot height while avoiding overlaps.

Examples

nmr <- load_example_nanomethresult()
#> Successfully matched 6 samples between data and annotation.
plot_region_heatmap(nmr, "chr7", 6703892, 6730431)