scater-plot-args {scater} | R Documentation

## 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`.

### Miscellaneous fields

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.

### See Also

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

[Package scater version 1.14.0 Index]