Skip to contents

Plot the methylation of a gene symbol specified within the exon(x) slot.

Usage

plot_gene(x, gene, ...)

# S4 method for class 'NanoMethResult,character'
plot_gene(
  x,
  gene,
  window_prop = 0.3,
  anno_regions = NULL,
  binary_threshold = NULL,
  avg_method = c("mean", "median"),
  spaghetti = FALSE,
  heatmap = TRUE,
  heatmap_subsample = 50,
  smoothing_window = 2000,
  gene_anno = TRUE,
  palette = ggplot2::scale_colour_brewer(palette = "Set1"),
  line_size = 1,
  mod_scale = c(0, 1),
  span = NULL
)

# S4 method for class 'ModBamResult,character'
plot_gene(
  x,
  gene,
  window_prop = 0.3,
  anno_regions = NULL,
  binary_threshold = NULL,
  avg_method = c("mean", "median"),
  spaghetti = FALSE,
  heatmap = TRUE,
  heatmap_subsample = 50,
  smoothing_window = 2000,
  gene_anno = TRUE,
  palette = ggplot2::scale_colour_brewer(palette = "Set1"),
  line_size = 1,
  mod_scale = c(0, 1),
  span = NULL
)

Arguments

x

the NanoMethResult or ModBamResult object.

gene

the gene symbol for the gene to plot.

...

additional arguments.

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.

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.

smoothing_window

the window size for smoothing the trend line.

gene_anno

whether to show gene annotation.

palette

the ggplot colour palette used for groups.

line_size

the size of the lines.

mod_scale

the scale range for modification probabilities. Default c(0, 1), set to "auto" for automatic limits.

span

DEPRECATED, use smoothing_window instead. Will be removed in next version.

Value

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

Details

This function plots the methylation data for a given gene. Since V3.0.0 NanoMethViz has changed the smoothing strategy from a loess smoothing to a weighted moving average. This is because the loess smoothing was too computationally expensive for large datasets and had a span parameter that was difficult to tune. The new smoothing strategy is controlled by the smoothing_window argument.

Functions

  • plot_gene(x = ModBamResult, gene = character): S4 method for ModBamResult

Examples

nmr <- load_example_nanomethresult()
plot_gene(nmr, "Peg3")