scater functions that plot points share a number of visualization parameters, which are described on this page.
Logical scalar, specifying whether a legend should be shown. Defaults to TRUE.
Integer scalar, specifying the font size. Defaults to 10.
Numeric scalar in [0, 1], specifying the transparency. Defaults to 0.6.
Numeric scalar, specifying the size of the points.
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
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.
Logical, should the median of the distribution be shown for violin plots?
Logical, should the outline of a violin plot be shown?
Logical, should a smoother be fitted to a scatter plot?
Logical, should standard errors for the fitted line be shown on a scatter plot when
Addititional fields can be added to the data.frame passed to ggplot by setting the
This allows users to easily incorporate additional metadata for use in further ggplot operations.
other_fields argument should be character vector where each string is passed to
retrieveCellInfo (for cell-based plots) or
retrieveFeatureInfo (for feature-based plots).
other_fields can be a named list where each element is of any type accepted by
This includes AsIs-wrapped vectors, data.frames or DataFrames.
Each additional column of the output data.frame will be named according to the
name returned by
If these clash with inbuilt names (e.g.,
colour_by), a warning will be raised and the additional column will not be added to avoid overwriting an existing column.
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