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 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)