General visualization parameters

Description

scater functions that plot points share a number of visualization parameters, which are described on this page.

Aesthetic parameters

add_legend:

Logical scalar, specifying whether a legend should be shown. Defaults to TRUE.

theme_size:

Integer scalar, specifying the font size. Defaults to 10.

point_alpha:

Numeric scalar in [0, 1], specifying the transparency. Defaults to 0.6.

point_size:

Numeric scalar, specifying the size of the points. Defaults to NULL.

jitter_type:

String to define how points are to be jittered in a violin plot. This is either with random jitter on the x-axis ("jitter") or in a “beeswarm” style (if "swarm", default). The latter usually looks more attractive, but for datasets with a large number of cells, or for dense plots, the jitter option may work better.

Distributional calculations

show_median:

Logical, should the median of the distribution be shown for violin plots? Defaults to FALSE.

show_violin:

Logical, should the outline of a violin plot be shown? Defaults to TRUE.

show_smooth:

Logical, should a smoother be fitted to a scatter plot? Defaults to FALSE.

show_se:

Logical, should standard errors for the fitted line be shown on a scatter plot when show_smooth=TRUE? Defaults to TRUE.

See Also

plotColData, plotRowData, plotReducedDim, plotExpression, plotPlatePosition, and most other plotting functions.