DimPlot: Dimensional reduction plot
In atakanekiz/Seurat3.0: Tools for Single Cell Genomics

Description Usage Arguments Value Note See Also Examples

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).

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 = "red", sizes.highlight = 1, na.value = "grey50",
  combine = TRUE, ...)

`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. By default, ggplot2 assigns colors
`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
`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
`combine`	Combine plots into a single gg object; note that if TRUE; themeing will not work when plotting multiple features
`...`	Arguments passed on to `CombinePlots` plots A list of gg objects ncol Number of columns legend Combine legends into a single legend choose from 'right' or 'bottom'; pass 'none' to remove legends, or `NULL` to leave legends as they are