Description Aesthetic parameters Distributional calculations Miscellaneous fields See Also
scater functions that plot points share a number of visualization parameters, which are described on this page.
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.
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
.
Addititional fields can be added to the data.frame passed to ggplot by setting the other_fields
argument.
This allows users to easily incorporate additional metadata for use in further ggplot operations.
The other_fields
argument should be character vector where each string is passed to retrieveCellInfo
(for cell-based plots) or retrieveFeatureInfo
(for feature-based plots).
Alternatively, other_fields
can be a named list where each element is of any type accepted by retrieveCellInfo
or retrieveFeatureInfo
.
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 retrieveCellInfo
or retrieveFeatureInfo
.
If these clash with inbuilt names (e.g., X
, Y
, colour_by
), a warning will be raised and the additional column will not be added to avoid overwriting an existing column.
plotColData
,
plotRowData
,
plotReducedDim
,
plotExpression
,
plotPlatePosition
,
and most other plotting functions.
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