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Plot aberrantly methylated regions

Source: R/plotAMR.R
plotAMR.Rd

`plotAMR` uses `ggplot2` to visualize aberrantly methylated regions (AMRs) at particular genomic locations.

Usage

plotAMR(
  data.ranges,
  amr.ranges,
  data.samples = NULL,
  window = 300,
  ignore.strand = FALSE,
  highlight = NULL,
  title = NULL,
  labs = c("genomic position", "beta value"),
  transform = c("identity", "log1p", "log10"),
  limits = NULL,
  breaks = NULL,
  verbose = TRUE
)

Arguments

data.ranges

A `GRanges` object with genomic locations and corresponding beta values included as metadata.

amr.ranges

An output of `getAMR` - a `GRanges` object that contain aberrantly methylated regions (AMRs).

data.samples

A character vector with sample names (a subset of metadata column names) to be included in the plot. If `NULL` (the default), then all samples (metadata columns) are included.

window

An optional integer constant to expand genomic ranges of the `amr.ranges` object (the default: 300).

ignore.strand

Boolean to ignore strand of AMR region. Default: FALSE.

highlight

An optional list of samples to highlight. If NULL (the default), will contain sample IDs from the `sample` metadata column of `amr.ranges` object.

title

An optional title for the plot. If NULL (the default), plot title is set to a genomic location of particular AMR.

labs

Optional axis labels for the plot. Default: c("genomic position", "beta value").

transform

Optional transformation of y-axis. Default: "identity" (no transformation).

limits

Optional limits of y-axis. When default (NULL), limits are c(NA,1) for `transform=="log10"` and c(0,1) otherwise.

breaks

Optional breaks of y-axis. When default (NULL), breaks are `10**(seq(from=-5, to=0, length.out=6))` for `transform=="log10"` and `seq(from=0, to=1, length.out=6)` otherwise.

verbose

Boolean to report progress and timings (default: TRUE).

Value

The output is a list of `ggplot` objects.

Details

For every non-overlapping genomic location from `amr.ranges` object, `plotAMR` plots and outputs a line graph of methylation beta values taken from `data.ranges` for all samples from `data.samples`. Samples bearing significantly different methylation profiles ('sample' column of `amr.ranges` object) are highlighted.

See also

getAMR for identification of AMRs, getUniverse for info on enrichment analysis, simulateAMR and simulateData for the generation of simulated test data sets, and `ramr` vignettes for the description of usage and sample data.

Examples

  data(ramr)
  plotAMR(data.ranges=ramr.data, amr.ranges=ramr.tp.unique[1])
#> Plotting 1 genomic ranges 
#> 100%
#> [0.182s]
#> $`chr1:2269871-2271665`

#> 
  library(gridExtra)
  do.call("grid.arrange",
          c(plotAMR(data.ranges=ramr.data, amr.ranges=ramr.tp.nonunique), ncol=2))
#> Plotting 5 genomic ranges 
#>  20% 40% 60% 80%100%
#> [0.365s]