Usage
dim.plot(object, reduction.use = "pca", dim.1 = 1, dim.2 = 2, cells.use = NULL, pt.size = 3, do.return = FALSE, do.bare = FALSE, cols.use = NULL, group.by = "ident", pt.shape = NULL)
Arguments
reduction.use
Which dimensionality reduction to use. Default is
"pca", can also be "tsne", or "ica", assuming these are precomputed.
dim.1
Dimension for x-axis (default 1)
dim.2
Dimension for y-axis (default 2)
cells.use
Vector of cells to plot (default is all cells)
pt.size
Adjust point size for plotting
do.return
Return a ggplot2 object (default : FALSE)
do.bare
Do only minimal formatting (default : FALSE)
cols.use
Vector of colors, each color corresponds to an identity
class. By default, ggplot assigns colors.
group.by
Group (color) cells in different ways (for example, orig.ident)
pt.shape
If NULL, all points are circles (default). You can specify any
cell attribute (that can be pulled with fetch.data) allowing for both different colors and different shapes on cells.