Create a new ggplot from a tidySingleCellExperiment

ggplot() initializes a ggplot object. It can be used to declare the input data frame for a graphic and to specify the set of plot aesthetics intended to be common throughout all subsequent layers unless specifically overridden.

# S3 method for SingleCellExperiment
ggplot(data = NULL, mapping = aes(), ..., environment = parent.frame())

Arguments

data

Default dataset to use for plot. If not already a data.frame, will be converted to one by fortify(). If not specified, must be supplied in each layer added to the plot.

mapping

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

...

Other arguments passed on to methods. Not currently used.

environment

Used prior to tidy evaluation.

Value

`ggplot`

Details

ggplot() is used to construct the initial plot object, and is almost always followed by a plus sign (+) to add components to the plot.

There are three common patterns used to invoke ggplot():

• ggplot(data = df, mapping = aes(x, y, other aesthetics))

• ggplot(data = df)

• ggplot()

The first pattern is recommended if all layers use the same data and the same set of aesthetics, although this method can also be used when adding a layer using data from another data frame.

The second pattern specifies the default data frame to use for the plot, but no aesthetics are defined up front. This is useful when one data frame is used predominantly for the plot, but the aesthetics vary from one layer to another.

The third pattern initializes a skeleton ggplot object, which is fleshed out as layers are added. This is useful when multiple data frames are used to produce different layers, as is often the case in complex graphics.

The data = and mapping = specifications in the arguments are optional (and are often omitted in practice), so long as the data and the mapping values are passed into the function in the right order. In the examples below, however, they are left in place for clarity.

Examples

library(ggplot2)
data(pbmc_small)
pbmc_small |> 
  ggplot(aes(groups, nCount_RNA)) +
  geom_boxplot()