plot_grange: Plot GRanges

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

Plot GRanges

Description

Plot GRanges

Usage

plot_grange(
  x,
  grange,
  anno_regions = NULL,
  binary_threshold = NULL,
  avg_method = c("mean", "median"),
  spaghetti = FALSE,
  heatmap = TRUE,
  heatmap_subsample = 50,
  gene_anno = TRUE,
  smoothing_window = 2000,
  window_prop = 0,
  palette = ggplot2::scale_colour_brewer(palette = "Set1"),
  line_size = 1,
  span = NULL
)

Arguments

x	the NanoMethResult object.
grange	the GRanges object with one entry.
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 equal to or below the threshold are set to 0.
avg_method	the average method for pre-smoothing at each genomic position. Data is pre-smoothed at each genomic position before the smoothed aggregate line is generated for performance reasons. The default is "mean" which corresponds to the average methylation fraction. The alternative "median" option is closer to an average within the more common methylation state.
spaghetti	whether or not individual reads should be shown.
heatmap	whether or not read-methylation heatmap should be shown.
heatmap_subsample	how many packed rows of reads to subsample to.
gene_anno	whether to show gene annotation.
smoothing_window	the window size for smoothing the trend line.
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.
palette	the ggplot colour palette used for groups.
line_size	the size of the lines.
span	DEPRECATED, use smoothing_window instead. Will be removed in next version.

Value

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

Examples

nmr <- load_example_nanomethresult()
plot_grange(nmr, GenomicRanges::GRanges("chr7:6703892-6730431"))

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