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, 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) ) PCAPlot(object, ...) TSNEPlot(object, ...) UMAPPlot(object, ...)
Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
Vector of cells to plot (default is all cells)
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
By default, ggplot2 assigns colors. We also include a number of palettes from the pals package.
DiscretePalette for details.
Adjust point size for plotting
Which dimensionality reduction to use. If not specified, first searches for umap, then tsne, then pca
Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class
Name of a metadata column to split plot by;
FetchData for more details
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.
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)
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)
Sets the seed if randomly shuffling the order of points.
Whether to label the clusters
Sets size of labels
Sets the color of the label text
Whether to put a box around the label text (geom_text vs geom_label)
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)
cols.highlight and other cells black (white if dark.theme = TRUE);
will also resize to the size(s) passed to
A vector of colors to highlight the cells as; will repeat to the length groups in cells.highlight
Size of highlighted cells; will repeat to the length groups in cells.highlight
Color value for NA points when using custom scale
Number of columns for display when combining plots
Combine plots into a single
ggplot object. If
FALSE, return a list of ggplot objects
Convert points to raster format, default is
automatically rasterizes if plotting more than 100,000 cells
Pixel resolution for rasterized plots, passed to geom_scattermore(). Default is c(512, 512).
Extra parameters passed to
patchworked ggplot object if
combine = TRUE; otherwise, a list of ggplot objects
For the old
do.identify functionality, please see
data("pbmc_small") DimPlot(object = pbmc_small) DimPlot(object = pbmc_small, split.by = 'ident')