Dimensional reduction plot — plot

Graphs the output of a dimensional reduction technique on a 2D scatter plot where each point is a cell and it's positioned based on the cell embeddings determined by the reduction technique. The function accepts both Seurat and SingleCellExperiment objects. For Seurat objects, cells are colored by their identity class by default, and for SingleCellExperiment objects, cells are colored by the first metadata column in colData(). The metadata variable used for coloring cells can be changed with the group_by parameter).

Usage

plot_reduction(
  object,
  dims = c(1, 2),
  cells = NULL,
  cols = NULL,
  pt_size = NULL,
  reduction = NULL,
  group_by = NULL,
  split_by = NULL,
  shape_by = NULL,
  order = NULL,
  shuffle = FALSE,
  seed = 1,
  label = FALSE,
  label_size = 4,
  label_color = "black",
  label_box = FALSE,
  repel = FALSE,
  cells_highlight = NULL,
  cols_highlight = "#DE2D26",
  sizes_highlight = 1,
  na_value = "grey50",
  ncol = NULL,
  combine = TRUE,
  raster = NULL,
  raster_dpi = c(512, 512)
)

Arguments

object: a Seurat object or a SingleCellExperiment object
dims: Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions i.e. c(1,2) to plot the first and second dimensions from the reduction results.
cells: Vector of cells to plot (default is all cells)
cols: Vector of colors, each color corresponds to an identity class. This may also be a single character or numeric value corresponding to a palette as specified by brewer.pal.info. By default, ggplot2 assigns colors. We also include a number of palettes from the pals package. See DiscretePalette for details.
pt_size: Adjust point size for plotting
reduction: Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca
group_by: Name of one or more metadata columns to group (color) cells by (for example, orig.ident). Unlike Seurat::DimPlot, "ident" may not be passed since the ident functionality is not supported by SingleCellExperiment objects. A metadata column name must be passed.
split_by: Name of a metadata column to split plot by. Unlike Seurat::DimPlot, "ident" may not be passed since the ident functionality is not supported by SingleCellExperiment objects. A metadata column name must be passed, or NULL to disable split plots.
shape_by: If NULL, all points are circles (default). You can specify any cell attribute (that can be pulled with FetchData) allowing for both different colors and different shapes on cells. Only applicable if raster = FALSE.
order: Specify the order of plotting for the idents. This can be useful for crowded plots if points of interest are being buried. Provide either a full list of valid idents or a subset to be plotted last (on top)
shuffle: Whether to randomly shuffle the order of points. This can be useful for crowded plots if points of interest are being buried. (default is FALSE)
seed: Sets the seed if randomly shuffling the order of points.
label: Whether to label the clusters
label_size: Sets size of labels
label_color: Sets the color of the label text
label_box: Whether to put a box around the label text (geom_text vs geom_label)
repel: Repel labels
cells_highlight: A list of character or numeric vectors of cells to highlight. If only one group of cells desired, can simply pass a vector instead of a list. If set, colors selected cells to the color(s) in cols_highlight and other cells black (white if dark.theme = TRUE); will also resize to the size(s) passed to sizes_highlight
cols_highlight: A vector of colors to highlight the cells as; will repeat to the length groups in cells_highlight
sizes_highlight: Size of highlighted cells; will repeat to the length groups in cells_highlight
na_value: Color value for NA points when using custom scale
ncol: Number of columns for display when combining plots
combine: Combine plots into a single patchworked ggplot object. If FALSE, return a list of ggplot objects
raster: Convert points to raster format, default is NULL which automatically rasterizes if plotting more than 100,000 cells
raster_dpi: Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).

Value

A patchworked ggplot object if combine = TRUE; otherwise, a list of ggplot objects

Details

The code for this function was from the Seurat Package and adapted for use with SingleCellExperiment objects.