Stacked bar plot of DEGs

plotDEGStackedBar(object, ...)

# S4 method for DESeqAnalysis
plotDEGStackedBar(
  object,
  i = NULL,
  direction = c("both", "up", "down"),
  orderBySize = FALSE,
  label = TRUE,
  fill = getOption(x = "acid.fill.discrete", default = getOption(x =
    "ggplot2.discrete.fill", default = AcidPlots::scale_fill_synesthesia_d())),
  flip = TRUE
)

Arguments

object

Object.

i

character, numeric, or NULL. Names or range of results. If set NULL, include all results.

direction

character(1). Include "both", "up", or "down" directions.

orderBySize

logical(1). Order contrasts by DEG set size.

label

logical(1). Label the number of DEGs per contrast on the plot.

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.

...

Additional arguments.

Value

ggplot.

Note

Updated 2020-09-21.

Examples

data(deseq) ## DESeqAnalysis ==== plotDEGStackedBar(deseq)