Stacked bar plot of DEGs

plotDEGStackedBar(object, ...)

# S4 method for DESeqAnalysis
plotDEGStackedBar(
  object,
  alpha = NULL,
  lfcThreshold = NULL,
  fill = getOption(x = "acid.fill.discrete", default =
    acidplots::scale_fill_synesthesia_d()),
  flip = TRUE
)

Arguments

object

Object.

...

Additional arguments.

alpha

numeric(1) or NULL. Adjusted P value ("alpha") cutoff. If left NULL, will use the cutoff defined in the object.

lfcThreshold

numeric(1) or NULL. Log fold change ratio (base 2) cutoff threshold. If left NULL, will use the cutoff defined in the object.

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())
flip

logical(1). Flip x and y axes. Recommended for plots containing many samples.

Value

Plot.

Note

Updated 2020-01-03.

Examples

data(deseq) plotDEGStackedBar(deseq)