Seurat (version 3.1.4)

DimPlot: Dimensional reduction plot

Description

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. By default, cells are colored by their identity class (can be changed with the group.by parameter).

Usage

DimPlot(
  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,
  label = FALSE,
  label.size = 4,
  repel = FALSE,
  cells.highlight = NULL,
  cols.highlight = "#DE2D26",
  sizes.highlight = 1,
  na.value = "grey50",
  ncol = NULL,
  combine = TRUE
)
PCAPlot(object, ...)
TSNEPlot(object, ...)
UMAPPlot(object, ...)

Arguments

object

Seurat object

dims

Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions

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); pass 'ident' to group by identity class

split.by

Name of a metadata column to split plot by; see FetchData for more details

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

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)

label

Whether to label the clusters

label.size

Sets size of labels

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

...

Extra parameters passed to DimPlot

Value

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

See Also

FeaturePlot HoverLocator CellSelector FetchData

Examples

# NOT RUN {
DimPlot(object = pbmc_small)
DimPlot(object = pbmc_small, split.by = 'ident')

# }