dim.plot: Dimensional reduction plot

In paodan/studySeu: Seurat : R toolkit for single cell genomics

Description

Graphs the output of a dimensional reduction technique (PCA by default). Cells are colored by their identity class.

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

object	Seurat object
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.

Value

If do.return==TRUE, returns a ggplot2 object. Otherwise, only graphical output.

paodan/studySeu documentation built on May 23, 2019, 3:06 p.m.