plot_region {NanoMethViz}R Documentation

Plot region

Description

Plot region

Usage

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

## S4 method for signature 'NanoMethResult,character,numeric,numeric'
plot_region(
  x,
  chr,
  start,
  end,
  anno_regions = NULL,
  binary_threshold = NULL,
  spaghetti = FALSE,
  span = NULL,
  window_prop = 0
)

## S4 method for signature 'NanoMethResult,factor,numeric,numeric'
plot_region(
  x,
  chr,
  start,
  end,
  anno_regions = NULL,
  binary_threshold = NULL,
  spaghetti = FALSE,
  span = NULL,
  window_prop = 0
)

Arguments

x

the NanoMethResult object.

chr

the chromosome to plot.

start

the start of the plotting region.

end

the end of the plotting region.

...

additional arguments.

anno_regions

the data.frame of regions to be annotated.

binary_threshold

the modification probability such that calls with modification probability above the threshold are set to 1 and probabilities equalt to or below the threshold are set to 0.

spaghetti

whether or not individual reads should be shown.

span

the span for loess smoothing.

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.

Value

a patchwork plot containing the methylation profile in the specified region.

a patchwork plot containing the methylation profile in the specified region.

Examples

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

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


[Package NanoMethViz version 2.0.0 Index]