Plot distribution of observed values

Usage

plotDistributions(
  se,
  selAssay = "counts",
  groupBy = NULL,
  plotType = "density",
  facet = FALSE,
  pseudocount = 0
)

Arguments

se: A SummarizedExperiment object, typically generated by summarizeExperiment().
selAssay: Character scalar specifying the assay in se to use for the plotting.
groupBy: Character scalar specifying a column from colData(se) to use for coloring or stratifying the plots.
plotType: Character scalar specifying the type of plot to construct. Either 'density', 'histogram' or 'knee'.
facet: Logical scalar, indicating whether or not to facet the plot by the values specified in the groupBy column.
pseudocount: Numeric scalar, representing the number to add to the observed values in the selAssay assay before plotting.

Value

A ggplot object.

Author

Charlotte Soneson

Examples

se <- readRDS(system.file("extdata", "GSE102901_cis_se.rds", 
                          package = "mutscan"))[1:200, ]
plotDistributions(se)
#> Warning: log-10 transformation introduced infinite values.
#> Warning: Removed 19 rows containing non-finite outside the scale range
#> (`stat_density()`).