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Plot gene methylation heatmap

Source: R/AllGenerics.R, R/plot_gene_heatmap.R
plot_gene_heatmap.Rd

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

Usage

plot_gene_heatmap(x, gene, ...)

# S4 method for class 'NanoMethResult,character'
plot_gene_heatmap(
  x,
  gene,
  window_prop = 0.3,
  pos_style = c("to_scale", "compact"),
  subsample = 50
)

# S4 method for class 'ModBamResult,character'
plot_gene_heatmap(
  x,
  gene,
  window_prop = 0.3,
  pos_style = c("to_scale", "compact"),
  subsample = 50
)

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.

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.

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_gene_heatmap(nmr, "Peg3")