"Novelty" refers to log10 genes detected per count.

plotNovelty(object, ...)

# S4 method for SingleCellExperiment
plotNovelty(object,
  geom = c("histogram", "ecdf", "violin", "ridgeline", "boxplot"),
  interestingGroups = NULL, min = 0L, fill = getOption(x =
  "acid.fill.discrete", default = acidplots::scale_fill_synesthesia_d()),
  trans = "identity", labels = list(title = "Novelty", subtitle = NULL,
  metricAxis = NULL, otherAxis = NULL))

Arguments

object

Object.

geom

character(1). Plot type. Uses match.arg() internally and defaults to the first argument in the character vector.

interestingGroups

character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.

min

numeric(1). Recommended minimum value cutoff.

fill

ggproto/ScaleDiscrete. Desired ggplot2 fill scale. Must supply discrete values. When set to NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_fill_manual().

To set the discrete fill palette globally, use:

options(acid.fill.discrete = ggplot2::scale_fill_viridis_d())
trans

character(1). Name of the axis scale transformation to apply.

For more information:

help(topic = "scale_x_continuous", package = "ggplot2")
labels

list. ggplot2 labels. See ggplot2::labs() for details.

...

Additional arguments.

Value

ggplot.

Note

Updated 2019-09-16.

Examples

data(SingleCellExperiment, package = "acidtest") ## SingleCellExperiment ==== object <- SingleCellExperiment object <- calculateMetrics(object)
#> Calculating 100 sample metrics.
#> 497 coding features detected.
#> 0 mitochondrial features detected.
plotNovelty(object)