plotDR: Plot reduced dimensions
In casanova-lab/iMUBAC: Integration of Multi-Batch Cytometry datasets

View source: R/plotDR.R

plotDR

R Documentation

Plot reduced dimensions

Description

Dimension reduction plot colored by expression values or column metadata. To avoid plotting too many dots as a vector graphic, geom_point_rast from ggrastr is used to internally replace the geom_point layer.

Usage

plotDR(
  sce,
  sce_bg = NULL,
  dimred = "UMAP",
  colour_by = "condition",
  text_by = NULL,
  facet_by = NULL,
  point_shape = 19,
  point_size = 0.5,
  point_alpha = 1,
  rasterize = T,
  ...
)

Arguments

`sce`	A `SingleCellExperiment` object.
`sce_bg`	An optional `SingleCellExperiment` object for background data. If provided, the data would be depicted in a light grey in a layer behind the main plot.
`dimred`	A character string specifying which dimension reduction to use. Should be one of `reducedDimNames(sce)`.
`colour_by`	A character string corresponding to a `colData(sce)` column. Specifies the color coding. If factor, a discrete color scale will be used. Otherwise, a cividis color scale will be applied by default.
`text_by`	A character string corresponding to a `colData(sce)` column. Specifies the text coding.
`facet_by`	A character string corresponding to a `colData(sce)` column. Specifies the faceting. Note: Users must provide a separate faceting command such as `lemon::facet_rep_grid`. Faceting does not occur internally.
`point_shape, point_size, point_alpha`	Parameters for the plot. Note: setting the shape to "." allows users to nicely plot a large number of dots.
`rasterize`	Logical. Whether the plot needs to be rasterized using ggrastr.
`...`	Additional arguments passed to `plotReducedDim` in scater.